STO-3G Basis Set Research Articles

Structural Features of Silatranes and Germatranes

In stabilization of the endo configuration of silatranes and germatranes, a major role is played not only by the Si (or Ge) and N atoms, but also by oxygen and other atoms of the atrane core, which is manifested in molecular orbital parameters. Calculation of the system of interacting methyltrimethoxysilane and trimethylamine shows that the energy of the system grows as the distance between the Si and N atoms is decreased from 5 to 2 A. The Si-N interaction in methylsilatrane, according to the calculations and precision X-ray diffraction studies, is the interaction of filled electronic shells and is electrostatic in nature. Analysis of the thermodynamic functions of formation of 1-methyl- and 1-hydroxysilatranes and -germatranes reveals an increase in the enthalpy and the decisive contribution of the entropy factors to stabilization of the reaction products. A 1H NMR study of ethylgermatrane in aqueous solution revealed its equilibrium with the hydro- lyzed form. The transition state in the first step of hydrolysis of methyl- and hydroxysilatranes and -germatranes was studied by methods of quantum chemistry (AM1, PM3; basis sets STO-3G, 6-31G, 6-31G*, 6-31G** B3LYP method).

Determination of the orientation of azathioprine adsorbed on a silver electrode by SERS and ab initio calculations

We report the SERS spectrum of azthioprine (AZA) on a silver electrode surface and the results of normal mode calculations using empirical and ab initio calculations of the 6-mercaptopurione (6-MP) component of AZA. The empirical calculations were done with a Urey-Bradley force field (UBFF) and the ab initio calculations with the STO-3G basis set using the UHF, MP2 and BLYP methods. From the difference between the SERS and solid spectra, we determined that AZA attaches edge-on to the surface through the N3 site on the 6-MP component of the molecule. The UBFF calculation on an Ag adatom-molecule model reproduced most of the main observed frequency shifts in the SERS spectrum. With a similar model, the ab initio calculations yielded frequency shifts in the same direction as the one observed for the in-plane normal modes, but they yielded opposite shifts for the out-of-plane normal modes. This phenomenon may be attributed to a face-on interaction of the 6-MP component with a neighboring adatom made possible by an inclination of the molecule on the surface.

Localized basis orbitals: minimization of 2-electron integrals array and orthonormality of basis set.

A new scheme for deriving localized basis orbitals (LBOs) and for obtaining integral transformations from the basis orbitals (BOs) to the LBOs has been introduced. The scheme was tested at the ab initio Hartree-Fock level using the STO-3G basis set. It has been revealed that it provides results that are close to the conventional ab initio approximations for various physical-chemical properties. At the same time, both the number of differential overlaps and the number of electron repulsion integrals (ERIs) grow with the system size notably slower than those calculated for the usual BOs. The power exponent for ERI/LBO is typically smaller by 0.3-0.6 than that for ERI/BO. The exponent reaches the value of 1.69 even for triglycine (24 atoms only), which represents a relatively small molecular model. Thus, the localization of the BOs (using LBOs) may result in additional improvements in efficiency even for electronically delocalized systems. It was shown that ERI/LBO is particularly efficient for systems with complex spatial structures (including conjugated species). The obtained results indicate that the proposed scheme could be included in computational methods targeted at calculating large molecular systems (which achieve linear scaling for more distant interactions). Neglecting ERI/LBO does not depend on the delocalization of the localized MO using ERI/LBO. The orthogonality and locality of the LBOs should make them useful in methods based on dividing the system into orthogonal subsystems.

Basis set dependent SCα exchange-only and exchange-correlation calculations

The SCα method [V. V. Karasiev and E.V. Ludeña, Phys. Rev. A 65, 062510 (2002)], has been implemented into a local version of the GAUSSIAN 98 program package. Using this modified code we have calculated total energies of selected atoms and molecules belonging to the G2 set within the KS-exchange-only and KS-exchange-correlation approximations. In these calculations we have used the exchange functionals LDA, B1, and PW91 and their SCα counterparts: SCα-LDA, SCα-B1, and SCα-PW91. The corresponding exchange-correlation functionals are B3LYP and SCα-B3LYP. We have also explored the basis set dependence of the SCα method by calculating the KS-exchange-only atomization energies using the following hierarchy of basis set functions: STO-3G, 6-31G*, 6-31G**, and 6-311++G(3df,3pd). The average error values of the SCα calculations (with respect to exact exchange EXX values) are 121, 133, and 128 kJ mol−1 (for the SCα-LDA, SCα-PW91, and SCα-B1 methods, respectively) for the STO-3G basis set; 20, 27, and 19 kJ mol−1 (for the SCα-LDA, SCα-PW91, and SCα-B1 functionals) for the 6-31G**; and 7, 10, 5 kJ mol−1, respectively, for the 6-311++G(3df,3pd). Hence, it is seen that the application of the SCα method to LDA, B1, and PW91 exchange functionals, yields atomization energies in close agreement with the EXX ones as long as a large enough basis set is used. Moreover, the SCα atomization energies calculations performed using the modified GAUSSIAN 98 code (for the spin unrestricted case), are much closer to the EXX values than those obtained using a spin-restricted numerical code.

Theoretical Modeling of the Stereoisomerization of Tetracoordinated Be(II) Bis(chelate) Complexes

Quantum-chemical (semiempirical MNDO and ab initio RHF SCF with an STO-3G basis set) calculations were performed for stereoisomerization of tetracoordinated Be(II) bis(chelate) complexes with BeN2O2 coordination unit. The most probable pathway for their monomolecular isomerization was found to involve, in agreement with experimental data, cleavage of a Be–N coordination bond to form a tricoordinated Be intermediate (dissociation–recombination mechanism) rather than a competitive polytopal rearrangement. The planar structure of the intermediate detected upon thermo- and photoexcitation of the complexes was predicted from our calculations.

X-Ray Crystallographic and Theoretical Studies of an Anticonvulsant Enaminone: Methyl 4-(4’-Bromophenyl)amino-6-methyl-2-oxocyclohex-3-en-1-oate

Objective: The aims of this study were to establish the structure of the potent anticonvulsant enaminone methyl 4-(4′-bromophenyl)amino-6-methyl-2-oxocyclohex-3-en-1-oate (E139), and to determine the energetically preferred conformation of the molecule, which is responsible for the biological activity. Materials and Methods: The structure of the molecule was determined by X-ray crystallography. Theoretical ab initio calculations with different basis sets were used to compare the energies of the different enantiomers and to other structurally related compounds. Results: The X-ray crystal structure revealed two independent molecules of E139, both with absolute configuration C11(S), C12(R), and their inverse. Ab initio calculations with the 6-31G, 3-21G and STO-3G basis sets confirmed that the C11(S), C12(R) enantiomer with both substituents equatorial had the lowest energy. Compared to relevant crystal structures, the geometry of the theoretical structures shows a longer C–N and shorter C=O distance with more cyclohexene ring puckering in the isolated molecule. Conclusion: Based on a pharmacophoric model it is suggested that the enaminone system HN–C=C–C=O and the 4-bromophenyl group in E139 are necessary to confer anticonvulsant property that could lead to the design of new and improved anticonvulsant agents.

The interaction of cis-2-butene over a 10-ring Brönsted acid site of zeolite: a theoretical study

We have investigated theoretically the interaction of cis-2-butene with a Brönsted acid site (BAS) embedded within a ring of 10 tetrahedral zeolite cluster (T10-OH). Calculations were performed at ab Initio SCF-MO level with the STO-3G basis set. Cs symmetry restriction was imposed for the optimization geometry of the T10-OH cluster, and no symmetry restriction was assumed for the cis-2-butene–HO-T10 interaction. This interaction first leads to the formation of a molecular complex, where the CC is weakly coordinated to the proton of the BAS. Then, a hexa-cyclic transition state involving the coordination of one C atom of the CC to one oxygen atom next neighbor of the OH group and the other C atom to the acid proton. Finally, an intermediate secondary alkoxy complex is formed. The alkoxide structure is a very stable complex, dominated by a covalent C–O bonding between the C atom and zeolite oxygen atoms.

π-Electron densities and resonance effects in benzene monoderivatives

The π-electron densities according to Mulliken or Löwdin in monosubstituted benzenes C 6H 5X with 30 different substituents X were calculated at a variable level from STO-3G to B3LYP/6-31l+G(d,p). Sum of the density, ∑ q π, at all C atoms or at all C and H atoms of the benzene ring was taken as an estimate of resonance ability of the substituent X and correlated with the standard scales of resonance constants σ R. The model is warrantable since ∑ q π at STO-3G obtained previously on monosubstituted ethenes correlate well with σ R derived from experiments. However, at higher levels of calculations, the correlations become stepwise worse with the greatest deviations for substituents not coplanar with the benzene ring. We attribute this deviation to a shortcoming of the valence-split basis set and held as probable that the π-electron density is represented better in the STO-3G basis set. For estimating the resonance constants, the present model has a merit compared to the substituted ethenes that it removes problems with ambiguous conformation. Nevertheless, comparison of various scales σ R revealed the limits of this approach.

Aqueous Solution Inclusion of the Nonionic Surfactant C 12 E 4 in β -Cyclodextrin: Implications of Micellization in Stoichiometry Determination and Model Calculations

The inclusion of α-n-dodecyl-ω-hydroxytetra(oxyethylene), C12E4, in β-cyclodextrin (βCD) has been studied in aqueous solution. Guest encapsulation is recognized by the upfield variations in the chemical shifts of the H3 and H5 inner protons of βCD, and the chemical shift differences of the H5 protons are used for determining the complex stoichiometry (2βCD : 1C12E4) by the continuous variation method. Self-association (micellization) of the surfactant molecules is considered, and the relative amount of surfactant involved in micellar systems at the stoichiometric point estimated. A two-layered integrated molecular orbital and molecular mechanics approach with the PM3 and UFF model chemistries for the guest and host, respectively, was used to perform full geometry optimizations and frequency calculations on the host-guest systems. Energies for the optimized structures were subsequently obtained by single point calculations at the Hartree–Fock level using the STO-3G basis set. These calculations showed that one C12E4 molecule encapsulated by a head-to-head βCD dimer is a stable model system in consonance with the experimentally determined stoichiometry, and that the 1 : 1 complex is not stable with respect to dissociation. In the stable 2 : 1 model system, the guest molecule is appreciably tilted with respect to the βCD dimer axis and presents a gradually bent alkylic chain in clear manifestation of conformational flexibility. Model calculations for βCD inclusion complexes of other oligo(oxyethylene) molecules further indicate that the number and strength of H⋯H intermolecular close contacts reflect the position and conformational flexibility of the guest hydrophobic chain inside βCD.

Composition dependent properties of GaAs clusters

We used a combination of first principles electronic structure calculation and semi-empirical methods to study the composition dependence of physical properties of small and medium sized GaAs clusters. Structures and physical properties of Ga 10− n As n ( n=0,1,2,…,10) clusters were determined using the ab initio Hartree–Fock method, with the STO-3G basis set. It was found that the structures of these clusters strongly depend on the composition and generally As-rich clusters are more stable than Ga-rich clusters. The dipole moment, HOMO-LUMO gap, vertical ionization energy, vertical electron affinity also depend on composition of the clusters and show an even/odd alteration with the number of Ga atoms (or As atoms) in the cluster.

Frequency-Dependent Polarizability of Boron Nitride Nanotubes: A Theoretical Study

In the present work, we have calculated the static and frequency-dependent polarizability tensors for a series of single-walled boron nitride nanotubes and compared them with corresponding results for carbon nanotubes. The calculations have been performed by employing a dipole−dipole interaction model based on classical electrostatics and an Unsold dispersion formula. In comparison, we have carried out ab intio calculations at the SCF level of the static polarizability of the smaller nanotubes with the STO-3G basis set. For the frequency-dependent polarizability of C60, we found excellent agreement among the most accurate SCF calculations in the literature, the interaction model, and experimental results. In particular, the frequency dependence is modeled accurately indicating that the interaction model is a useful tool for studying the frequency dependence of materials. For the nanotubes, we observe the same trends in the interaction model and in the SCF STO-3G results when the number of atoms is increas...

The molecular structure and electronic spectrum of the C@C 60 endohedral complex: An ab initio study

We performed ab initio quantum-chemical studies at the HF and B3LYP levels of theory to determine the geometry and electronic spectra of the C@C 60 complex. The STO-3G and 6-31G(d) basis sets were employed. Two different types of stable conformations for the endohedral atom related to the centers of five- and six-member rings were found. The estimated potential barrier between those conformations is small; under certain conditions, the endohedral atom can transfer from one location in the molecular cage to another. The influence of the location of endohedral carbon atom on the electronic spectrum of C 60 is discussed. © 2001 by Elsevier Science Inc.

A theoretical study of subphthalocyanine and its nitro- and tertbutyl-derivatives

The unsubstitute subphthalocyanine (SubPc) and their tertbutyl- ( tertbutyl-SubPc) and nitro-(nitro-SubPc) derivatives have been theoretically studied at Hartree–Fock (HF) and Density Functional Theory (DFT) levels using STO-3G and 6-31G basis sets. The geometric optimization of the molecules was carried out. The calculated geometry for SubPc agrees with experimental X-ray data. No significant geometrical changes with respect to SubPc were observed in the tertbutyl-SubPc and nitro-SubPc macrocycles. B–Cl distance systematically changes with the electron donor/acceptor properties of the peripheral substituents. The calculated dipole moments reproduce very well the experimental values, whereas the atomic charges reveal the polar character of the SubPc macrocycle. An extensive study of some frontier orbitals was performed. The present calculations reproduce the breakdown of Gouterman's four-orbital model in SubPcs, this effect being less dramatic in the DFT description. The nodal patterns for the two highest occupied molecular orbitals and the two lowest unoccupied molecular orbitals obtained from different computational methods exhibit important differences, but in general an explanation for some of the most important aspects of the chemical reactivity of the SubPcs can be put forward.

DNA Photoionization and Alkylation Patterns in the Interior of Guanine Runs

Of the DNA bases, guanine has the smallest ionization potential (IP). The recent combined use of experimental gas-phase photoelectron data and self-consistent field (SCF) and post-SCF descriptions has provided new information about the energetics of guanine ionization at the nucleotide and dinucleotide levels (Fernando, H.; Papadantonakis, G. A.; Kim, N. S.; LeBreton, P. R. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 5550−5555. Kim, N. S.; Zhu, Q.; LeBreton, P. R. J. Am. Chem. Soc. 1999, 121, 11516−11530). The energetic matching of the highest occupied π orbitals and the π interaction which occurs in regions of stacked guanines (G runs) give rise to sequence-specific regions of low IP. This is described by a Koopmans analysis of results from ab initio SCF calculations with 6-31G*, 6-31G, 3-21G, and STO-3G basis sets and with ZINDO semiempirical calculations on oligonucleotides and oligonucleotide models. At the ab initio 3-21G SCF level, model calculations indicate that the lowest IP of guanine in a double-st...

Boron Quasicrystals and Boron Nanotubes: Ab Initio Study of Various B96 Isomers

The rhombohedral unit cells of α-boron crystals and of hypothetical α-boron quasicrystals were investigated by applying ab initio quantum-chemical methods. The atomic decorations of such unit cells are generally based on a suitable arrangement of eight boron icosahedra, and thus the mechanism of their cohesion was simulated by relaxing a B96 supercluster composed of icosahedral boron clusters located at the vertices of the rhombohedral unit cells. Also, several alternative structures of B96 clusters were proposed and compared to the rhombohedral phases. To this end, total energies of those structures were computed on the basis of all-electron calculations at the Hartree–Fock self-consistent field level of theory using the standard STO3G basis set. Due to the large number of degrees of freedom, the geometries of all isomers were optimized under reasonable symmetry constraints, but using analytical gradient methods. The resulting total energies show that segments of nanotubes and quasiplanar sheets turn out to be more stable than the unit cells of α-boron (quasi) crystals, indicating new kinds of materials.

High performance computing on the Cray T3E and IBM SP2 systems with the parallel version of GAUSSIAN 94

Benchmark tests were performed to study the efficiency of parallel computations on a Cray T3E 1200 and IBM SP2 systems with the parallel version of commercial quantum chemistry set of programs GAUSSIAN 94. Representative molecular systems (a complex between nitrobenzene and the hydrated surface of clay minerals, a complex of guanosine phosphate with a hydrated magnesium cation, and a fullerene molecule) have been investigated. These species represent the systems of current interest in the fields of environmental, biological, and material science as well as general chemistry. Our benchmark tests were designed to investigate a performance of a popular Hartree–Fock (HF) and DFT/B3LYP levels of theory with the STO-2G, STO-3G, 3-21G*, 4-31G, 6-31G, and 6-31G(d) basis sets. The wallclock time and efficiency of parallelization for links 502 and 703 were studied.

Ab initio and semi-empirical studies of the static polarizability and the second hyperpolarizability of diamond: finite T d symmetry models from CH 4 to C 281H 172

The mean static polarizability and second hyperpolarizability of a series of diamond-like molecules capped by hydrogen atoms have been calculated. Both semi-empirical (MNDO, AM1, PM3) and ab initio Hartree–Fock (with basis sets STO-3G, 3-21G, 6-31G ∗∗ ) methods have been used. The results enable the determination of the mean polarizability of diamond and an estimation of the second hyperpolarizability. The values are consistent with the little experimental data available.

Ab initio MO studies on protonation mechanism of ethylene over catalyst HZSM-5

Four calculation models (I–IV) were proposed for studying the protonation mechanism of ethylene over catalyst HZSM-5. Ab initio SCF-MO calculations were carried out at the STO-3G basis set level. From the calculation results of geometry optimization and Mulliken population of these models, it has been shown that the cis-four-centered reaction mechanism (model I) is the most reasonable one, while the vertical complex reaction mechanism (model II) is of no effect, and models III and IV are possible for the terminal radical absorption.

Ab initio MO LCAO SCF simulation of molecular and electronic structure of η5-π-C60H5XCp (X=Fe, Si) complexes

The problem of existence of η5-π-complexes of unsubstituted fullereneI h -C60 and its cyclopentadienyl type derivative C60H5 . is discussed.Ab initio MO LCAO SCF calculations of hypothetical sandwich systems η5-π-C60H5XCp (X=Fe (1a), Si (1b)), the cationic complex C60FeCp+ of unsubstituted C60, and the C60H5 . radical were performed in the STO-3G and 3-21G basis sets. In the1a, 1b, and C60H5 . systems, hydrogen atoms are attached to carbon atoms of fullerenei h -C60 at α-positions relative to the same pentagonal face (pent *). In η5-complexes, XCp species are also coordinated to this face. According to calculations in the 3-21G basis set, the Fe-pent * bond energy in complex1a is much higher than those of similar bonds in1b and in the η5-π-C60FECp+ cation (117 kcal mol−1 vs. 37 and 64 kcal mol−1, respectively) and is 7 kcal mol−1 higher than the Fe−Cp bond energy in the classical sandwich system FeCp2. The Fe…C pent* and Fe…CCp distances in complex1a are slightly shorter than the Fe…C distance in the ferrocene molecule. The spin populations in the C60H5 . radical are almost completely localized on the atoms of thepent * face, which must favor the formation of η5-π-complexes of this radical.

Classical Dynamics of the Hydrogen Atom and Muonium Trapped in Diamond Clusters: A Direct Ab-initio Dynamics Study

Abstract Direct ab-initio dynamics calculations have been carried out for hydrogen and muonium (Mu) trapped in a C10H16 cluster model in order to elucidate qualitatively the finite temperature effect on f-value ( = |ΦH(0)|2/|Φvac(0)|2, where |Φvac(0)|2 is the contact spin density on H nuclei in vacuum and |ΦH(0)|2 is one in the model cluster). In the dynamics calculations, a split-valence type basis set (31G) was used for the central hydrogen atom and a minimal basis set STO-3G for the cluster model. All atoms were treated as classical particles moving on the ab-initio full dimensional surface including all degrees of freedom calculated at the Hartree–Fock level. Three temperatures, 300, 600, and 1000 K, are chosen as simulation temperatures. The averaged f-values are obtained for each temperature by using MP2/3-21G* level. In addition, the f-value corresponding to 0 K is calculated by the static ab-initio MO calculation (i.e., without dynamics effect). The f-values for 0, 300, 600, and 1000 K were calculated to be 1.224, 1.211, 1.200, and 1.185, respectively, indicating that the f-value linearly decreases with increasing temperature. The f-value was simply expressed by the equation f (T) = f(T = 0 K)[1−0.325 × 10−5 T]. The present calculations indicated that the f-value is slightly affected by the thermal activation, the shift of f-value is small. This work is the first attempt to calculate the finite-temperature effect on the f-value at the ab-initio dynamics level.