On the additivity of basis set effects in some simple fluorine containing systems

The reactions F + H₂ → HF + H, HF → H + F, F → F⁺ + e^? and F + e^? → F^? were used as simple test cases to assess the additivity of basis set effects on reaction energetics computed at the MP4 level. The 6-31G and 6-311G basis sets were augmented with 1, 2, and 3 sets of polarization functions, higher angular momentum polarization functions, and diffuse functions (27 basis sets from 6-31Gd, p) to 6-31 ++ G(3df, 3pd) and likewise for the 6-311G series). For both series substantial nonadditivity was found between diffuse functions on the heavy atom and multiple polarization functions (e.g., 6-31 + G(3d, 3p) vs. 6-31 + G(d, p) and 6-31G(3d, 3p)). For the 6-311G series there is an extra nonadditivity between d functions on hydrogen and multiple polarization functions. Provided that these interactions are taken into account, the remaining basis set effects are additive to within ±0.5 kcal/mol for the reactions considered. Large basis set MP4 calculations can also be estimated to within ±0.5 kcal/mol using MP2 calculations, est. E_MP4(6-31 ++ G(3df, 3pd)) ≈ E_MP4(6-31G(d, p)) + E_MP2(6-31 ++ G(3df, 3pd)) – E_MP2(6-31G(d, p)) or E_MP4(6-31 + G(d, p) + E_MP2(6-31 ++ G(3df, 3pd)) – E_MP2(6-31 + G(d, p)) and likewise for the 6-311G series.     

An ab initio study of the structure,dissociation energy,and heat of formation of Na2S

The equilibrium geometries and fundamental frequencies of Na₂S are calculated at HF, MP2(FC, FU), and MP3 with the 6–31G(d) basis set and at HF and MP2(FC, FU) with the 6–31G(d) basis set, respectively. The total energy at MP2(FU)/6–31G(d)-optimized geometry is computed at MP4 with 6–311G(d, p), 6–311 + G(d, p), and 6–311G(2df, p), at QCISD(T)/6–311G(d, p), and at MP2/6–311G(3df, 2p) levels, respectively. The dissociation energy, the atomization energy, and the heat of formation for Na₂S are evaluated using the G1 and G2 models. The calculated results indicated that Na₂S in its ground state was a bent structure (C_2v). Electron correlation corrections on the bending angle are very significant. The equilibrium geometrical parameters are R_e(Na-S) = 2.45 Å and ∠Na-S-Na = 111.13° at the MP2(FU)/6–31G(d) level. The theoretically estimated dissociation energy, total atomization energy, and heat of formation are 67.07, 117.55, and 0.35 kcal mol⁻¹, respectively, at 298.15 K. © 1997 John Wiley & Sons, Inc.     

Proton affinities of molecules containing nitrogen and oxygen: comparing ab initio and semiempirical results to experiments

We report a comparison of theoretical and experimental proton affinities at nitrogen and oxygen sites within a series of small molecules. The calculated proton affinities are determined using the semiempirical methods AM 1, MNDO , and PM 3; the ab initio Hartree–Fock method at the following basis levels: 3-21G //3-21G , 3-21+G //3-21G , 6-31G *//6-31G *, and 6-31+G (d, p)//6-31G *; and Møller–Plesset perturbation calculations: MP 2/6-31G *//6-31G *, MP 3/6-31G *//6-31G *, MP 2/6-31G +(d, p)//6-31G *, MP 3/6-31G +(d, p)//6-31G *, and MP 4(SDTQ )/6-31G +G (d, p)//6-31G *. The semiempirical methods have more nonsystematic scatter from the experimental values, compared to even the minimal 3-21G level ab initio calculations. The thermodynamically corrected 6-31G *//6-31G * proton affinities provide acceptable results compared to experiment, and we see no significant improvement over 6-31G *//6-31G * in the proton affinities with any of the higher-level calculations. © 1992 John Wiley & Sons, Inc.     

Basis set dependence,precision, and accuracy of full ab initio gradient optimizations of molecular structures of nonstrained hydrocarbons. I. CC bond lengths

Different highly accurate experimental determinations of molecular structures (ED: r_g and r⁰_α, MW: r₀, r_s, and r_z, and X-ray distances) of 14 unstrained hydrocarbons have been linearly correlated with corresponding self-consistent field Hartree Fock (SCF HF) ab initio full gradient-optimized structures. From the eight applied basis sets (STO -3G, STO -6G; 3-21G, 4-31G, 6-31G, 6-311G; 6-31G*, and 6-31G**) the 6-31G basis set, although not best regarding total energies, yields statistically the most precise regression equation, which allows the prediction of ED r_g CC distances as reliable as the best experimental determinations. Surprisingly the accuracy of all calculated CC distances (measured as difference Δ between calculated CC distances and experimental ED r_g values) depends linearly on bond distances, with the largest deviations being observed for triple bonds. This seems to be a clear indication of different influences of correlation effects on calculated geometries which are neglected in the applied HF treatment. The linear regression equations presented here allow the prediction of any kind of experimental CC distance parameters for each of the eight basis sets considered. Even experimentally unknown r_e CC distances may be predicted from these single determinantal HF optimizations.     

Determination of maximum loading capacity of polyamidoamine (PAMAM) dendrimers and evaluation of Cu55 dendrimer‐encapsulated nanoparticles for catalytic activity

Spectrophotometric titrations provide information about the interior of the polyamidoamine (PAMAM) dendrimers, and therefore how nanoparticles are encapsulated. In this work, binding studies were performed to determine maximum loading capacities (N) of hydroxyl terminated G4, G5, and G6 PAMAM dendrimers with Cu²⁺ ions. The values of N found via spectrophotometric titrations were 16.22, 31.86, and 57.36 for G4‐OH, G5‐OH, and G6‐OH, respectively. The determination of loading capacity was also done using Viva spin filtration, and the results were found to be in agreement with those found via spectrophotometric titrations. From the binding isotherm, the values of equilibrium constant (K′) were determined and found to be 0.0488 (G4‐OH), 0.0291 (G5‐OH), and 0.0158 (G6‐OH). Owing to instability of G4‐OH (Cu₁₆), G5‐OH (Cu₃₂), and G6‐OH (Cu₅₇) dendrimer‐encapsulated nanoparticles (DENs) synthesized, G6‐OH (Cu₅₅) DENs of average size 2.6 ± 0.3 nm were prepared and were found to be relatively stable. Thus G6‐OH (Cu₅₅) catalyst was evaluated for the reduction of 4‐nitrophenol and was found to be catalytically active toward reduction of 4‐nitrophenol. Reaction kinetics of 4NP reduction was thoroughly studied in light of the Langmuir‐Hinshelwood kinetic model, and surface rate k, and the adsorption rates K_4NP, and K_BH4 were determined. The reaction was performed at different temperatures, which further expanded the study into determination of thermodynamic (ΔH^‡, ΔS^‡, ΔG^‡, and E_A) parameters.     

Chemotaxonomy of Triterpenoid Pattern of HPLC of Ganoderma lucidum and Ganoderma tsugae

Three strains of Ganoderma tsugae (CCRC36065, CCRC37034, CCRC37038) and three strains of Ganoderma lucidum (CCRC36021, CCRC37029, CCRC37033) were cultivated. Their triterpenoid patterns of the fruit body were analyzed by reverse phase HPLC using a gradient elution of acetonitrile/2% acetic acid (1/4 and 1/2). The triterpenoid patterns of G. tsugae and G. lucidum are different. But similar 2 and 3 dimensional patterns are obtained among three strains of G. tsugae. Different patterns are found among different strains of G. lucidum. Ganoderic acid A( 1 ), B( 2 ), C( 3 ) and D( 4 ) were isolated from the ethanol extract of G. tsugae.     

Symbiosis between Microorganisms from Kombucha and Kefir: Potential Significance to the Enhancement of Kombucha Function

Gluconacetobacter sp. A4 (G. sp. A4), which had strong ability to produce d-saccharic acid 1, 4 lactone (DSL), was the key functional bacteria isolated from the kombucha preserved. This paper investigated the interaction between G. sp. A4 and ten different strains of lactic acid bacteria (LAB) obtained from kefir. The result suggested that the LAB promoted DSL production of G. sp. A4 to different extents, ranging from 4.86% to 86.70%. Symbiosis between G. sp. A4 and LAB was studied. LAB’s metabolites, xylitol, and acetic acid, were utilized by G. sp. A4, and it promoted the growth of G. sp. A4 and yield of DSL. Therefore, in developing starter cultures for kombucha fermentation process, a mixed flora of LAB and G. sp. A4 would be the optimal combination.     

Authentication of Gentiana straminea Maxim. and its substitutes based on chemical profiling of iridoids using liquid chromatography with mass spectrometry

A liquid chromatography–electrospray ionization–ion‐trap mass spectrometry (MSⁿ) method was established and applied for authentication of Gentiana straminea from the four substitutes, G. tibetica, G. lhassica, G. waltonii and G. robusta, based on chemical profiling of the principal iridoid glucosides aided by a quadrupole time‐of‐flight mass spectrometry. The fragmentation pathways of the three representative iridoid glucosides, loganic acid, gentiopicroside and sweroside, were investigated by MSⁿ analysis in negative ion mode, which assisted the characterization of analogs detected in the chromatographic profiling of the tested Gentiana species. In total, 25 iridoids were identified or tentatively characterized from G. straminea and four substitutes, in which 7‐O‐(4′′‐O‐glucosyl)coumaroyl‐loganic acid and 7‐O‐coumaroyl‐loganic acid are diagnostic in G. straminea and can serve as the proposed chemical markers to discriminate it from morphologically similar substitutes.     

Comparison of sterols and fatty acids in two species of <Emphasis Type="Italic">Ganoderma</Emphasis>

Background  

Two species of Ganoderma, G. sinense and G. lucidum, are used as Lingzhi in China. Howerver, the content of triterpenoids and polysaccharides, main actives compounds, are significant different, though the extracts of both G. lucidum and G. sinense have antitumoral proliferation effect. It is suspected that other compounds contribute to their antitumoral activity. Sterols and fatty acids have obvious bioactivity. Therefore, determination and comparison of sterols and fatty acids is helpful to elucidate the active components of Lingzhi.     

Metallocene–methylaluminoxane catalysts for olefin polymerizations. III. Reduction of η5-cyclopentadienyl trichlorides of titanium and zirconium

The reactions occurring between the components of metallocene and methylaluminoxane (MAO) catalyst leading to the reduction of the former were studied by electron paramagnetic resonance (EPR). At low Al/Zr ratios, C_pZrCl₃ (C_p = η⁵-cyclopentadienyl) was reduced to simple trivalent Zr species (g = 1.998, a(⁹¹Zr) = 12.3 G) without other superhyperfine splittings. At higher Al/Zr ratios the reactions proceed further to form two CpZr(III) hydrides (g = 1.991, a(H) = 5.5 G; and g = 2.00, a(H) = 3 G). Two CpTi(III) hydrides were also produced by the reaction of MAO with CpTiCl₃ (g = 1.989, a(H) = 7.4 G, a(Ti) = 8 G; and, g = 1.995, a(H) = 4.5 G, a(Ti) = 8 G). In the case of Cp^*TiCl₃ (Cp^* = η⁵-pentamethyl cyclopentadienyl) initially a multitude of paramagnetic species were formed. After long reaction time the final products show EPR features consistent with two η³: η⁴-(1,2,3-trimethyl-4,5-dimethylene cyclopentadienyl)hydrido Ti(III) species: the abundant one with g = 1.999, (H, sextet) = 9.5 G, a(Ti) = 9.5 G, and a weaker one of g = 1.975, a(H) = 4.8 G. All the five protons of these species and as well as those in the Cp hydrido complexes of Ti and Zr undergo facile H? D exchanges with D₂. MAO is important in the formation of these hydrides because they are not formed by trimethyl aluminum reduction. The presence of tetrahydrofuran suppresses the hydride formation. The possible structures for the hydrido species and reactions producing them are discussed.     

The electronic structure of small lithium clusters

Ab initio molecular orbital calculations using the STO-6G and STO6-21G basis sets have been performed for the cluster series Li _n ⁺ , Li _n , and Li _n ^– (wheren=2–7). Thirty-two optimized structures are discussed and reported, many of which (especially for the anionic structures) have not yet been considered. The calculations suggest that for all three species the optimum geometries are planar. Of the two levels of theories that were investigated, STO-6G//STO-6G and STO6-21G//STO-6G, the latter hybrid theory was found to be less reliable. In particular, for the anionic structures these calculations should provide a platform from which more sophisticated, i.e., configuration interaction, geometry optimization can be performed.     

Quantum-Chemical Analysis of Coordination of Dimethylsulfoxide Molecules to Sodium and Potassium Cations

Coordination of dimethylsulfoxide molecules to the sodium and potassium cations was investigated by HF/6-31G(d)//HF/6-31G(d) and DFT(B3LYP/6-31G(d)) quantum-chemical methods. The coordination numbers of Na⁺ and K⁺ are found to be five and six, respectively. Thermal effects of complexation were calculated for each stage of the process; these were found to be 197.8, 160.1, 106.9, 88.0, 53.9 [HF/6-31G(d)] and 195.0, 158.5, 108.9, 95.7, 60.0 kJ/mole [B3LYP/6-31G(d)] for Na⁺ (one to five DMSO molecules, respectively); 146.6, 118.7, 90.2, 68.9, 70.0, 49.0 [HF/6-31G(d)] and 144.0, 117.4, 91.7, 78.9, 78.6, 56.4 kJ/mole [B3LYP/6-31G(d)] for K⁺ (one to six DMSO molecules, respectively). Structural parameters and charge distributions are given for the complexes. It is shown that solvation of sodium and potassium cations by DMSO molecules is preferable to solvation by water molecules.     

Combined bond-polarization basis sets for accurate determination of dissociation energies. II. Basis set superposition error as a function of the parent basis set

The effect of the parent basis set on the basis set superposition error caused by bond functions is investigated systematically. An important difference between BSSE at the SCF and correlated levels is pointed out. Three new basis sets are defined, denoted 6-311 + G(d,p)B, 6-311 + G(2d,p)B, and 6-311 + G(2df,p)B. BSSE for the first-row hydrides seems to increase uniformly with increasing atomic number of the central atom. Expansion of the valence part of the basis set from 6-31G to 6-311G, as well as adding f functions, has a significant effect on the BSSE. Additional BSSEs incurred by bond functions are less than or equal to 1 kcal/mol for the 6-311 + G(2df,p)B basis set. For the dissociation energies of the first-row hydride species, agreement with experiment within only a few kcal/mol can be obtained even without resorting to isogyric reaction cycles. For high-quality calculations, adding bond functions seems to have definite advantages over expanding the polarization space beyond the [2d1f] level.     

Theoretical and experimental studies of the electrochemistry of <Emphasis Type="Italic">p</Emphasis>-aminophenol on a golden electrode

The geometric parameters, vibrational frequencies, and thermochemical values of p-quinonimine (p-AQ) and p-aminophenol (p-AP) were computed ab initio (IIF) and by the density functional theory (DFT) method with the 6-31G(d, p) basis set. Cyclic voltammetry with a golden electrode of p-AP solutions in phosphate buffers at pH 7.30 showed that the standard electrode potential of half reaction for p-QI and p-AP was 0.728 V. The standard electrode potentials of half reactions for p-QI and p-AP were calculated using the free energies and solvation energies of p-QI, p-AP, p-benzoquinone (p-BQ), and hydroquinone (p-HQ). The results showed that the standard electrode potential of half reaction for p-QI and p-AP was 0.743 V at the B3LYP/6-31G(d, p) level and 0.755 V at the HF/6-31G(d, p) level. The standard electrode potentials computed at the B3LYP/6-31G(d, p) and HF/6-31G(d, p) levels were close to their experimental values. The article is published in the original.     

A study of internal rotations and vibrational spectra of oxiranemethanol (glycidol)

The conformational stability and the C–O and O–H internal rotations in oxiranemethanol were investigated at the DFT-B3LYP/6-311G**, MP2/6-311G** and MP4(SDQ)/6-311G** levels of theory. Three minima were predicted in the CCOH potential energy scans of the molecule to have relative energies of about 2 kcal/mol or less and all were calculated to have real frequencies upon full optimization of structural parameters at the DFT and the MP2 levels of calculations. The Cg1 (H bond inner) conformation was predicted to be the lowest energy conformation for oxiranemethanol in excellent agreement with an earlier microwave study. The equilibrium mixture was calculated from Gibb's free-energy changes to be about 79% Cg1, 17% G1g and 3% Gg1 at the B3LYP/6-311G** level and about 87% Cg1, 11% G1g and 2% Gg1 at the MP2/6-311G** level for oxiranemethanol at 298.15 K. No conclusive evidence was obtained for the presence of high-energy form in the liquid phase of oxiranemethanol. The vibrational frequencies of oxiranemethanol in its three stable forms were computed at the B3LYP level and complete vibrational assignments were made for the lowest energy Cg1 form on basis of calculated and experimental data of the molecule.     

Theoretical studies on the conformations of selenamides

Ab initio HF/6-31+G*, MP2/6-31+G*, B3LYP/6-31+G* level calculations have been performed on HSe-NH₂ to estimate the Se-N rotational barriers and N-inversion barriers. Two conformers have been found withsyn andanti arrangement of the NH₂ hydrogens with respect to Se-H bond. The N inversion barriers in selenamide are 1.65, 2.47, 1.93 kcal/mol and the Se-N rotational barriers are 6.58, 6.56 and 6.12 kcal/mol respectively at HF/6-31+G*, MP2/6-31+G* and B3LYP/6-31+G* levels respectively. The n_N →Σ *_Se-H negative hyperconjugation is found to be responsible for the higher rotational barriers.     

Basis-Set dependence of exterior electron distributions of molecular orbitals

Interior electron densities are divided from exterior electron densities (EED ), when an effective boundary is introduced. The EED concept was used to study the quality of wavefunction tails; the basis-set dependence of ab initio MO for NH₃ was studied from EED . The EED for the nonbonding orbital (3a₁) increases dramatically with the size of basis sets, whereas that for the bonding orbital (1e) shows saturation even at the double zeta class. Although inclusion of polarization functions always gives the better total energy the EED (3a₁) may either increase or decrease or decrease depending on the choice of the smaller or the larger exponents. The conventional choice of the polarization functions for 6-311G* and 6-311G* was found to yield worse wavefunction tails than the case of 6-311G. Much better results were obtained with the more diffuse polarization functions. The (11s7p)/[5s4p] set designed for Rydberg states as well as the 6-311 + G set proposed for negative ions gave excellent results comparable to the case of the near Hartree-Fock calculation with 56 CGTO. Considerable improvements were also achieved for 4-31G and 6-311G sets, when the exponent for the outermost s-type function was modified. The largest EED (3a₁) gave the best agreement with the experimental ratio of EED 's derived from Penning ionization electron spectroscopy.     

Synthesis and Spectroscopic Characterisation of a New Class of Heterobimetallic Zirconocene(IV) Compounds

Reactions of Cp₂ZrCl₂ with homometallic complexes of aluminium containing one residual hydroxy group Al(OGO)(OGOH) and Al(L)(OGOH) [where G=G¹=CMe₂CMe₂ (1a); G=G²=CMe₂CH₂CHMe (1b); G= G³=CMe₂CH₂CH₂CMe₂ (1c) and L=L¹=OC₆H₄CH=NCH₂CH₂O, G=G¹ (2a); L=L¹, G=G² (2b); L=L¹, G=G³ (2c); L=L²=OC₁₀H₆CH=NCH₂CH₂O, G=G¹ (2d); L=L², G=G² (2e); L=L², G=G³ (2f)] in THF using Et₃N as HCl acceptor affords novel heterobimetallic compounds of the types Al(OGO)₂Zr(Cl)Cp₂ and Al(L)(OGO)Zr(Cl)Cp₂, respectively. All of these derivatives have been characterised by elemental analyses, molecular weight measurements, and spectroscopic [IR, NMR (¹H and ²⁷Al)] studies.     

FeII Metallohelices Stabilize DNA G-Quadruplexes and Downregulate the Expression of G-Quadruplex-Regulated Oncogenes

DNA G-quadruplexes (G4s) have been identified within the promoter regions of many proto-oncogenes. Thus, G4s represent attractive targets for cancer therapy, and the design and development of new drugs as G4 binders is a very active field of medicinal chemistry. Here, molecular biophysics and biology methods were employed to investigate the interaction of chiral metallohelices with a series of four DNA G4s (hTelo, c-myc, c-kit1, c-kit2) that are formed by the human telomeric sequence (hTelo) and in the promoter regions of c-MYC and c-KIT proto-oncogenes. We show that the investigated water-compatible, optically pure metallohelices, which are made by self-assembly of simple nonpeptidic organic components around Fe^II ions and exhibit bioactivity emulating the natural systems, bind with high affinity to G4 DNA and much lower affinity to duplex DNA. Notably, both enantiomers of a metallohelix containing a m-xylenyl bridge ( 5 b ) were found to effectively inhibit primer elongation catalyzed by Taq DNA polymerase by stabilizing G4 structures formed in the template strands containing c-myc and c-kit2 G4-forming sequences. Moreover, both enantiomers of 5 b downregulated the expression of c-MYC and c-KIT oncogenes in human embryonic kidney cells at mRNA and protein levels. As metallohelices also bind alternative nucleic acid structures, they hold promise as potential multitargeted drugs.     

Is tetrahedral H42+ a minimum? Anomalous behavior of popular basis sets with the standard p exponents on hydrogen

The nature of the tetrahedral H₄²⁺ stationary point (minimum or triply degenerate saddle) depends remarkably upon the theoretical level employed. Harmonic vibrational analyses with, e.g., the 6-31G** (and 6-31 + +G**) and Dunning's [4s2p1d;2s1p] [D95(d,p)] basis sets using the standard p exponent suggest (erroneously) that the T_d geometry is a minimum at both the HF and MP2 levels. This is not the case at definitive higher levels. The C₃H₄²⁺ structure with an apical H is another example of the failure of the calculations with the 6-31G**, 6-311G**, and D95(d,p) basis sets. Even at MP2/6-31G** and MP2/ cc-pVDZ levels, the C_3v structure has no negative eigenvalues of the Hessian. Actually, this form is a second-order saddle point as shown by the MP2/6-31G** calculation with the optimized exponent. The D_4h methane dication structure is also an example of the misleading performance of the 6-31G** basis set. In all these cases, energy-optimized hydrogen p exponents give the correct results, i.e., those found with more extended treatments. Optimized values of the hydrogen polarization function exponents eliminate these defects in 6-31G** calculations. Species with higher coordinate hydrogens may also be calculated reliably by using more than one set of p functions on hydrogen [e.g., the 6-31G(d,2p) basis set]. Not all cases are critical. A survey of examples, also including some boron compounds, provides calibration. © 1993 John Wiley & Sons, Inc.