STO-3G Basis Set Research Articles

SIMULATION OF VINPOCETINE RELEASE PROCESS FROM MICROCAPSULES WITH HYDROPHOBIC SHELL

Nowadays microcapsules are widely spread in different industries. Microcapsules with vitamins, etheric and fatty oils are included into different cosmetics (creams, gels, serums). Microencapsulated probiotics are used in foods and fodder additives in veterinary. An important field of application of microencapsulation in pharmacy is the combination in the total dosage of drugs that are incompatible when mixed in free form. The aim of work is a comparative analysis of thermodynamic characteristics of vinpocetine release from the melt of beeswax and cacao butter 3:2 into water, solution of hydrochloric acid 0.01 M and ethanol. Materials and methods . For simulation of the process of vinpocetine release from the melt into different environments models component models of the studied systems were built and their atom charges were calculated by quantum-chemical method. Spatial models of the components were built in Hyper Chem 8.01. As an initial state for the thermodynamic characteristics of the calculation of vinpocetine release from the melt, a conformation of «melt-vinpocetine» system was used after thermodynamic equilibration by molecular dynamics simulation in Bioeurica program for 5 ns. For isolated systems a vibrational analysis was performed with the use of unrestricted Hartree-Fock method in STO-3G basis set in Orca 4.0 program. Results and discussion . Vinpocetine release from the melt of beeswax and cacao butter 3:2 into water with different pH values and to ethanol depends on its solubility in these environments, and also on solubility of the melt. Conclusion. The performed study of vinpocetine release from the melt of beeswax and cacao butter 3:2 by molecular dynamics simulation demonstrates the opportunity of vinpocetine release into water with pH=2 and into ethanol. The obtained results make it possible to assume a lower degree of vinpocetine release from the melt into ethanol compared with the solution of hydrochloric acid 0,01 M.

Polycaprolactone/Amino-β-Cyclodextrin Inclusion Complex Prepared by an Electrospinning Technique.

Electrospun scaffolds of neat poly-ε-caprolactone (PCL), poly-ε-caprolactone/β-cyclodextrin inclusion complex (PCL/β-CD) and poly-ε-caprolactone amino derivative inclusion complex (PCL/β-CD-NH2) were prepared by the electrospinning technique. The obtained mats were analyzed by a theoretical model using the Hartree–Fock method with an STO-3G basis set, and characterized by X-ray diffraction (XRD), field emission scanning electron microscopy (FESEM), Fourier transform infrared spectroscopy-attenuated total reflectance (FTIR-ATR), differential scanning calorimetry (DSC), confocal-Raman spectroscopy, proton nuclear magnetic resonance (1HNMR) and contact angle measure (CA). Different mixtures of solvents, such as dimethylformamide (DMF)-tetrahydrofuran (THF), dichlormethane (DCM)-dimethyl sulfoxide (DMSO) and 2,2,2-Trifluoroethanol (TFE), were tested in the fiber preparation. The results indicate that electrospun nanofibers have a pseudorotaxane structure and when it was prepared using a 2,2,2-Trifluoroethanol (TFE) as solvent, the nanofibers were electrospun well and, with the other solvents, fibers present defects such as molten fibers and bead-like defects into the fiber structure. This work provides insights into the design of PCL/β-CD-NH2 based scaffolds that could have applications in the biomedical field.

F2 storage by confinement inside carbon nanotubes

Theoretical calculations have been achieved to study the interaction between the confined F2 molecule along the nanotube axis and perpendicular to it and armchair (n,n) single-walled carbon nanotubes with n = 4, 5, 6, 7, and 8 and the zig-ag nanotube (9,0) using the density functional theory method with the CAM-B3LYP functional and both cc-pVQZ and STO-3G basis sets. The interaction of the F2 molecule with the nanotube is different according to the molecular orientation, the chirality of the carbon nanotube, and the confinement space extension. These results interpreted by means of van der Waals interactions reveal anisotropic and competitive behavior at the nanometric level. The π electrons of the nanotube interact with the lone pairs of F2 highlighting its lateral polarizability. The encapsulated F2 molecule is stable along and perpendicular to the nanotube (5,5) and (6,6) axis. The best stabilization energy is obtained fornanotube (5,5) at the perpendicular position using the cc-pVQZ basis set.

Intermediate electrostatic field for the generalized elongation method.

An intermediate electrostatic field is introduced to improve the accuracy of fragment-based quantum-chemical computational methods by including long-range polarizations of biomolecules. The point charge distribution of the intermediate field is generated by a charge sensitivity analysis that is parameterized for five different population analyses, namely, atoms-in-molecules, Hirshfeld, Mulliken, natural orbital, and Voronoi population analysis. Two model systems are chosen to demonstrate the performance of the generalized elongation method (ELG) combined with the intermediate electrostatic field. The calculations are performed for the STO-3G, 6-31G, and 6-31G(d) basis sets and compared with reference Hartree-Fock calculations. It is shown that the error in the total energy is reduced by one order of magnitude, independently of the population analyses used. This demonstrates the importance of long-range polarization in electronic-structure calculations by fragmentation techniques.

The BRUSH algorithm for two-electron integrals on GPU

This Letter presents a new algorithmic method developed to evaluate two-electron repulsion integrals based on contracted Gaussian basis functions in a parallel way. This new algorithm scheme provides distinct SIMD (single instruction multiple data) optimized paths which symbolically transforms integral parameters into target integral algorithms. Our measurements indicate that the method gives a significant improvement over the CPU-friendly PRISM algorithm. The benchmark tests (evaluation of more than 108 integrals using the STO-3G basis set) of our GPU (NVIDIA GTX 780) implementation showed up to 750-fold speedup compared to a single core of Athlon II X4 635 CPU.

Valence state parameters of all transition metal atoms in metalloproteins--development of ABEEMσπ fluctuating charge force field.

To promote accuracy of the atom-bond electronegativity equalization method (ABEEMσπ) fluctuating charge polarizable force fields, and extend it to include all transition metal atoms, a new parameter, the reference charge is set up in the expression of the total energy potential function. We select over 700 model molecules most of which model metalloprotein molecules that come from Protein Data Bank. We set reference charges for different apparent valence states of transition metals and calibrate the parameters of reference charges, valence state electronegativities, and valence state hardnesses for ABEEMσπ through linear regression and least square method. These parameters can be used to calculate charge distributions of metalloproteins containing transition metal atoms (Sc-Zn, Y-Cd, and Lu-Hg). Compared the results of ABEEMσπ charge distributions with those obtained by ab initio method, the quite good linear correlations of the two kinds of charge distributions are shown. The reason why the STO-3G basis set in Mulliken population analysis for the parameter calibration is specially explained in detail. Furthermore, ABEEMσπ method can also quickly and quite accurately calculate dipole moments of molecules. Molecular dynamics optimizations of five metalloproteins as the examples show that their structures obtained by ABEEMσπ fluctuating charge polarizable force field are very close to the structures optimized by the ab initio MP2/6–311G method. This means that the ABEEMσπ/MM can now be applied to molecular dynamics simulations of systems that contain metalloproteins with good accuracy.

The Investigation of Sequence-dependent Interaction of Messenger RNA Binding to Carbon Nanotube

To investigate carbon nanotubes (CNTs) as gene delivery vehicles, it is essential to characterize their interactions with mRNA. Messenger RNA is a powerful tool for controlling the expression of genes in biomedical applications. In the present report, we study the interactions of single-walled CNT with three codons of mRNA(UGC,GAC,CAG) by using MM, AM1,HF and DFT (B3LYP) methods with STO-3G and 3-21G basis sets in gas phase. To estimate the stability of Nanotubes- mRNA complexes total energy of the systems were determined. The varieties of obtained energy data suggest the relation between the stability of complexes as this order: CAG > GAC > UGC. According to the ability of NMR in providing detailed information about the structure and chemical environment of molecules, this technique has been carried out by supposing gauge-included atomic orbital (GIAO). Considering on the calculated results of NMR chemical shift consist of σiso, σaniso, Δσ, δ and η that are very sensitive to small changes in molecular geometry and chemical environments and the results of energy reveal that the characteristic's variety and the stability of these complexes is depend on the specific mrna base and nucleotide sequences. We can predict that diseases with special mutation and gene sequences are the better aim for special kinds of treatment. Current observations will allow the implementation of new strategies in the development of CNT: mRNA complexes as effective gene therapy.

Efficient Modeling of NMR Parameters in Carbon Nanosystems.

Rapid growth of nanoscience and nanotechnology requires new and more powerful modeling tools. Efficient theoretical modeling of large molecular systems at the ab initio and Density Functional Theory (DFT) levels of theory depends critically on the size and completeness of the basis set used. The recently designed variants of STO-3G basis set (STO-3Gel, STO-3Gmag), modified to correctly predict electronic and magnetic properties were tested on simple models of pristine and functionalized carbon nanotube (CNT) systems and fullerenes using the B3LYP and VSXC density functionals. Predicted geometries, vibrational properties, and HOMO/LUMO gaps of the model systems, calculated with typical 6-31G* and modified STO-3G basis sets, were comparable. The (13)C nuclear isotropic shieldings, calculated with STO-3Gmag and Jensen's polarization consistent pcS-2 basis sets, were also identical. The STO-3Gmag basis sets, being half the size of the latter one, are promising alternative for studying (13)C nuclear magnetic shieldings in larger size CNTs and fullerenes.

Alternative Approach to Calculate Two-Center Overlap Matrix through Deformed Exponential Function

In this work, we propose an alternative approach to evaluate two-center overlap integrals. It is computationally more efficient than the standard procedure and is based on the deformed exponential function. In the new procedure, the CPU time to calculate each element of the overlap matrix (Sμ,ν) is constant and independent of the number of Gaussian primitives (NG), whereas in the usual procedure this time increases, formally, with NG2. To evaluate the accuracy of the proposed methodology, we computed different molecular properties such as dipole moments, hardness values, atomic charges, multicenter bond indices, group indices, and some thermodynamic properties. In this work, all calculations were performed using a minimal STO-6G basis set and WTBS and the double-ζ Pople split-valence 6-31G basis set on the Hartree–Fock (HF) and post-HF approximations. The integrals were parametrized for the atoms of the first two rows of the periodic table. All calculations were performed in the general ab initio quantum chemistry package GAMESS, where the integrals were implemented.

A Systematic Approach for Understanding Slater–Gaussian Functions in Computational Chemistry

A systematic way to understand the intricacies of quantum mechanical computations done by a software package known as “Gaussian” is undertaken via an undergraduate research project. These computations involve the evaluation of key parameters in a fitting procedure to express a Slater-type orbital (STO) function in terms of the linear combination of Gaussian-type orbital (GTO) functions. A procedure for the optimization process based on the Newton–Raphson method is developed and is applied to STO-2G and STO-3G basis sets. Satisfactory results obtained by this procedure are used to illustrate the importance of ab initio computations for inclusion in the chemistry or physics undergraduate curriculum. Programming languages such as Python and Maple were employed to obtain the results.

Synthesis and computational study of two new glycoluril clips containing benzocrown ether side walls

Two new glycoluril-derived molecular clips containing benzocrown ether side walls have been synthesized via reaction of a glycoluril scaffold with two bromomethylated benzocrown ethers. The molecular geometry of their most stable structures were investigated with density functional theory at the B3LYP level of theory using STO-3G, 6-31G, and 6-311G basis sets. Then based on the obtained computer-optimized structures, the binding properties of one clip with some 5-substituted resorcinols have been calculated.

A Promising Tool to Achieve Chemical Accuracy for Density Functional Theory Calculations on Y-NO Homolysis Bond Dissociation Energies

A DFT-SOFM-RBFNN method is proposed to improve the accuracy of DFT calculations on Y-NO (Y = C, N, O, S) homolysis bond dissociation energies (BDE) by combining density functional theory (DFT) and artificial intelligence/machine learning methods, which consist of self-organizing feature mapping neural networks (SOFMNN) and radial basis function neural networks (RBFNN). A descriptor refinement step including SOFMNN clustering analysis and correlation analysis is implemented. The SOFMNN clustering analysis is applied to classify descriptors, and the representative descriptors in the groups are selected as neural network inputs according to their closeness to the experimental values through correlation analysis. Redundant descriptors and intuitively biased choices of descriptors can be avoided by this newly introduced step. Using RBFNN calculation with the selected descriptors, chemical accuracy (≤1 kcal·mol−1) is achieved for all 92 calculated organic Y-NO homolysis BDE calculated by DFT-B3LYP, and the mean absolute deviations (MADs) of the B3LYP/6-31G(d) and B3LYP/STO-3G methods are reduced from 4.45 and 10.53 kcal·mol−1 to 0.15 and 0.18 kcal·mol−1, respectively. The improved results for the minimal basis set STO-3G reach the same accuracy as those of 6-31G(d), and thus B3LYP calculation with the minimal basis set is recommended to be used for minimizing the computational cost and to expand the applications to large molecular systems. Further extrapolation tests are performed with six molecules (two containing Si-NO bonds and two containing fluorine), and the accuracy of the tests was within 1 kcal·mol−1. This study shows that DFT-SOFM-RBFNN is an efficient and highly accurate method for Y-NO homolysis BDE. The method may be used as a tool to design new NO carrier molecules.

The route to highly stable MeBxNyCz molecular wheels. I. The features of preliminary results

By means of ab initio quantum chemical methods we have determined the energies and electronic structures of molecular wheels TiBn, TiBnN10−n, TiCnN10−n and TiCnB10−n (for n = 0–10). The ground state energies and the corresponding spin states of each atom, cluster and molecular wheel were calculated first in the framework of Hartree-Fock self-consistent-field (HF-SCF) using minimal and more accurate basis sets STO-3G and 6-31G. Computations at higher level and accuracy are processing in a follow-up study. The most stable wheel system is TiCnB10−n (for n = 5–10). Thereof particularly highly stable is the TiC5B5 molecular wheel followed by the TiC6B4. At the HF-SCF/6-31G level, however, we have calculated the wheel system MeC5B5 considering for Me, the first row of transition metal atoms Me = Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, and Zn. The molecular wheel MeC5B5 favours Sc atom at the centre, but also Ti and Fe are the next favoured atoms.

Transportation of single wall carbon nanotube (SWCNT) through the cell membrane

Carbon nanotubes (CNTs) are very common in medical research and are being highly studied in the fields of biosensing methods for disease treatment and efficient drug delivery and health monitoring. The transportation of open-end Single wall carbon nanotube (SWCNT) through the cell membrane widely investigated because of many advantages. In our recent study, extensive quantum mechanical (QM) calculation of electronic structure of open-end of SWCNT and transportation of single wall carbon nanotube through the cell membrane have been administered in vacuum media using GAUSSIAN 98 software. Our results manifested that the interaction of open-end of SWCNT has minimum value of energy interaction and then most structural stability in vacuum. We assayed effects of vacuum on transportation of SWCNT through the cell membrane with using B1LYP and Hartree Fock (HF) methods at STO-3G, 3-21G, 6-31G levels of theory. Also, we demonstrated the total atomic charges of dense region calculated STO-3G, 3-21G and 6-31G basis sets in vacuum with HF method. The calculated values showed negative charge at this site. The O and S atoms at interaction site produced negative charge because they have high electron affinity. Key words: Single wall carbon nanotube (SWCNT), quantum mechanical (QM), STO-3G, 3-21G and 6-31G basis.

Predicting pKa Values of Substituted Phenols from Atomic Charges: Comparison of Different Quantum Mechanical Methods and Charge Distribution Schemes

The acid dissociation (ionization) constant pK(a) is one of the fundamental properties of organic molecules. We have evaluated different computational strategies and models to predict the pK(a) values of substituted phenols using partial atomic charges. Partial atomic charges for 124 phenol molecules were calculated using 83 approaches containing seven theory levels (MP2, HF, B3LYP, BLYP, BP86, AM1, and PM3), three basis sets (6-31G*, 6-311G, STO-3G), and five population analyses (MPA, NPA, Hirshfeld, MK, and Löwdin). The correlations between pK(a) and various atomic charge descriptors were examined, and the best descriptors were selected for preparing the quantitative structure-property relationship (QSPR) models. One QSPR model was created for each of the 83 approaches to charge calculation, and then the accuracy of all these models was analyzed and compared. The pK(a)s predicted by most of the models correlate strongly with experimental pK(a) values. For example, more than 25% of the models have correlation coefficients (R²) greater than 0.95 and root-mean-square errors smaller than 0.49. All seven examined theory levels are applicable for pK(a) prediction from charges. The best results were obtained for the MP2 and HF level of theory. The most suitable basis set was found to be 6-31G*. The 6-311G basis set provided slightly weaker correlations, and unexpectedly also, the STO-3G basis set is applicable for the QSPR modeling of pK(a). The Mulliken, natural, and Löwdin population analyses provide accurate models for all tested theory levels and basis sets. The results provided by the Hirshfeld population analysis were also acceptable, but the QSPR models based on MK charges show only weak correlations.

An analysis of SCF and geometry convergence for diatomic molecules

Abstract A geometry and SCF convergence study of Hartree-Fock calculations using the 6-31G* basis set is carried out on the set of all possible diatomic molecules formed from atoms with Z≤36. The utility of Hartree-Fock calculations using the smaller STO-3G basis set to improve the convergence behavior is demonstrated.

QM Scoring Function and its Application to TOP1 Inhibitors

between the amino acids and the DNA were replaced with hydrogen atoms to make the complex sufficiently small for the QM treatment. Three different sets of calculations were performed for each complex: TOP1_fragment-DNA_fragment–ligand (G Complex ), TOP1_fragment-DNA_fragment (G TOP1 ), and ligand (G Ligand ). Frequency calculations were introduced to calculate the entropic contribution to the total free energy. The calculations were carried out using GAUSSIAN03. 16 During the QM calculation, the coordinates of the heavy atoms of TOP1 and DNA parts were fixed whereas the other coordinates were relaxed. The total energy and interaction energy were evaluated at the HF level using the STO-3G and 4-21G basis sets. Relatively small basis sets were used because the systems are still fairly large for the application of QM. The binding energy was calculated as follows:

Highly Sensitive and Selective “Turn-on” Calcium Cation Sensing from a Dendronic Terthiophene Tetraethylene Glycol (TEG) Molecule

A molecule consisting of a branched or dendronic terthiophene with tetraethylene glycol moiety (3T5O) was synthesized for highly sensitive and selective calcium ion detection in solution. The sulfur atoms of the terthiophene dendron moiety contribute to the metal-ligand complexation of calcium cations. The modification of the terthiophene dendrons with a hydroxyl-terminated tetraethylene glycol (TEG) group produces a twisted intramolecular charge transfer (TICT) event in which the terthiophene moiety is conformationally twisted, affecting its chromophoric and fluorophoric activity. This twisted conformation resulted in an increase in emission intensity at 320 nm, at the same time producing a blue shift in the absorption spectra. This process enabled a "turn-on" system for calcium ion detection compared to most "turn-off" systems involving a quenching route. The intensity of the emission is related to saturation of the terthiophene moiety at a concentration of 3T5O:[Ca(2+)] 1:4, of ∼1 × 10(-8) M, which indicates high sensitivity for calcium cations. No response with other cations such as Na(+), K(+), and Mg(2+) was observed, which also indicates high selectivity for the system. Conformational analysis of the 3T5O and the twisted terthiophene dendron geometry was done by semiempirical PM3 modeling. In an effort to distinguish specific interactions between monovalent and divalent cations and the 3T5O, restricted Hartree-Fock level calculations using the STO-3G basis set were also performed. The calculations correlated with the experimental results.

A time-dependent semiempirical approach to determining excited states

We study a time-dependent semiempirical method to determine excitation energies, TD-PM3. This semiempirical method allows large molecules to be treated. A Linear-response Chebyshev approach yields the TD-PM3 spectrum very efficiently. Spectra and excitation energies were tested by comparing it with the results obtained using TD-DFT (Time Dependent-Density Functional Theory), using both small and large basis sets. They were also compared to PM3-CI, Time Dependent-Hartree Fock using the STO-3G basis set, and to experiment. TD-PM3 results generally match better the large-basis set calculations than the small-basis TD-DFT do; excitation energies are almost always accurate to within about 20% or less, except for a few small molecules. Accuracy improves as the molecules get larger.

Quantum-chemical prediction of the scandium extraction power of phosphinic acids

The extraction power of phosphinic acids (PAs) toward scandium was predicted on the basis of PA characteristics (dissociation enthalpies and energies, Lowdin and Mulliken effective charges on the oxygen and phosphorus atoms of the phosphoryl group) and the energy of scandium complexation with PAs during extraction, which were calculated by quantum-chemical methods with the use of the HyperChem Release 8.0.4 (Hypercube Inc.) and PC GAMESS version 6.4 software. It was demonstrated that the use of the minimal basis set STO-3G provided the highest multiple correlation coefficient of log KSc (KSc is the concentration constant of scandium extraction) with the Lowdin effective charge of the oxygen atom and the dissociation energy of PAs (R = 0.963).