STO-3G Basis Set Research Articles

Calculation of MP2 and Coupled-Cluster Molecular Properties Using the q-Integral Method

The main purpose of this paper is to report results of quantum mechanical calculation of the H(2) system using the q-Integral method with correlation corrections to the SCF (Self Consistent Field) wave functions included through the Møller-Plesset second-order perturbation (MP(2)) and Coupled-Cluster (CC) theory. Using the q-Integral method, we evaluated potential energy curves, rovibrational spectroscopy constants, rovibrational spectra, interatomic equilibrium distance and longitudinal static hyper(polarizability). All calculations were carried out through the STO-3G, STO-6G, and double-zeta (DZV) atomic basis set. The q-Integral method was implemented in the source code of the general ab initio quantum chemistry package GAMESS.

Size extensivity of the variational reduced-density-matrix method

With the density-matrix variational method, the ground-state energy of a many-electron system is calculated by minimizing the energy expectation value subject to the selected representability conditions for the second-order reduced-density matrix (2-RDM). There is a lack of size extensivity under the $P$, $Q$, and $G$ conditions of this method by applying to $M$ noninteracting atoms and molecules up to $M=32$; ${\text{Be}}_{M}$, ${({\text{CH}}_{4})}_{M}$, and ${({\text{N}}_{2})}_{M}$. The energy per molecule $(E/M)$ monotonically decreases as $M$ increases, showing the lack of size extensivity in this method. The inextensive contributions to energies are $3\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}4}$ and $3\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}3}\text{ }\text{a}\text{.u}\text{.}$ for ${({\text{CH}}_{4})}_{M}$ and ${({\text{N}}_{2})}_{M}$ using the STO-6G basis set, respectively. In the examples studied, $E/M$ approaches a finite value as $M\ensuremath{\rightarrow}\ensuremath{\infty}$. The intermolecular elements of 2-RDMs do not satisfy the cumulant expansion.

Accounting for the exact degeneracy and quasidegeneracy in the automerization of cyclobutadiene via multireference coupled-cluster methods

The automerization of cyclobutadiene (CBD) is employed to test the performance of the reduced multireference (RMR) coupled-cluster (CC) method with singles and doubles (RMR CCSD) that employs a modest-size MR CISD wave function as an external source for the most important (primary) triples and quadruples in order to account for the nondynamic correlation effects in the presence of quasidegeneracy, as well as of its perturbatively corrected version accounting for the remaining (secondary) triples [RMR CCSD(T)]. The experimental results are compared with those obtained by the standard CCSD and CCSD(T) methods, by the state universal (SU) MR CCSD and its state selective or state specific (SS) version as formulated by Mukherjee et al. (SS MRCC or MkMRCC) and, wherever available, by the Brillouin-Wigner MRCC [MR BWCCSD(T)] method. Both restricted Hartree-Fock (RHF) and multiconfigurational self-consistent field (MCSCF) molecular orbitals are employed. For a smaller STO-3G basis set we also make a comparison with the exact full configuration interaction (FCI) results. Both fundamental vibrational energies-as obtained via the integral averaging method (IAM) that can handle anomalous potentials and automatically accounts for anharmonicity- and the CBD automerization barrier for the interconversion of the two rectangular structures are considered. It is shown that the RMR CCSD(T) potential has the smallest nonparallelism error relative to the FCI potential and the corresponding fundamental vibrational frequencies compare reasonably well with the experimental ones and are very close to those recently obtained by other authors. The effect of anharmonicity is assessed using the second-order perturbation theory (MP2). Finally, the invariance of the RMR CC methods with respect to orbital rotations is also examined.

An ab initio study of the reaction pathway between a mitomycin fragment model and ammonia

Ab initio self-consistent field calculatins with an STO-6G basis set are performed in order to determine the activation energy of a nucleophilic attack by ammonia on the double bond of 2-formyl-4-amino-2-pyrroline, a mitomycin fragment model.

Electronic studies of the pyrrolidine molecule with aziridine ring

The pyrrolidine ring with an aziridine ring attached to it is studied, using ab-initio calculations with a STO-6G basis set. The aziridine ring hydrolysis energy is calculated, comparing the energy of the cis product's to the trans products' energy.

Theoretical investigations of the structure of potential inhibitors of the enzyme glyoxalase-I

Ab initio calculations using an sto-3G basis set are reported for a variety of known inhibitors of glyoxalase I (esculetin, isoesculetin, ascorbic acid, maltol, etc.). Experimental investigations suggest that these inhibitors function as transition state analogs; and molecular electrostatic potential maps of the substrate of the enzyme, a variety of possible intermediates, and the inhibitors were calculated and compared. It was found that the most effective inhibitors have the distance R between the OH minima of ˜3.4 A. Suggestions for other inhibitors are made on the basis of the calculations.

Molecular determinants for recognition of phencyclidine derivatives at muscarinic cholinergic receptors

We report the results of a study combining synthetic organic chemistry, NMR spectroscopy, pharmacologic testing of receptor affinity, and theoretical calculations to elucidate the molecular determinants for the activity of phencyclidine (PCP) on the muscarinic type of acetylcholine receptor (M-ACh-R). A series of analogs was prepared to test the hypothesis that rigidity of the phenyl ring rotation and its relative orientation with respect to the cyclohexyl ring are responsible for PCP recognition at M-ACh-R. Quantum mechanical calculations (SCF with STO-3G basis sets) as well as molecular mechanics calculations (with the MM2 program) were used to elucidate the structures and define the conformations of the compounds, the rigidity of the phenyl ring arrangement, and the structural determinants for the recognition of these drugs at M-ACh-R. Pharmacologic testing indicates that there is no preference for an axial or equatorial configuration of the phenyl ring for interaction with M-ACh-R. This is consistent with the ACh-like interaction pharmacophore defined in earlier studies. However, the increased barrier to rotation of the phenyl ring in these compounds, compared to PCP, explains their increased affinity for M-ACh-R. A novel derivative in which the phenyl bisects the cyclohexyl ring rather than being perpendicular to it, as in the active PCP analogs, is not recognized at the M-ACh-R. Although it contains the same structural groups as PCP, we show that the stereochemistry of this derivative makes it incompatible with the ACh-like interaction pharmacophore.

Theoretical studies on the activation mechanism of the histamine H2-receptor: The guanidine substitution and its role in the partial agonism of N(alpha)-guanylhistamine

Histamine [2-(4-imidazolyl)ethylamine, HA] is a neurotransmitter that was shown to act on two different receptors, the H1- and H2-receptors. Structure-activity considerations made it possible to identify molecular determinants for the action of drugs on the H2-receptors. A key probe of the resulting hypothesis relating molecular structure to activity on these receptors is its ability to explain the action of partial agonists which are pharmacologic intermediates between agonists and antagonists. We therefore studied the molecular structure and properties of N (alpha)-guanylhistamine [2-(4-imidazolyl)ethylguanidine, NAGHA], which differs from histamine by a substitution of the side chain amine by a guanidine group. To understand how the substitution with the guanidine determines this change in properties, we also studied separately the molecular structure of guanidine and guanidinium in various tautomeric forms, with geometry optimization and several different basis sets. The results suggest the preferred site of protonation and interaction of NAGHA with the negative site of the H2-receptor. For N(3)-H and N(1)-H tautomers of the neutral and cationic species of NAGHA, we did complete geometry optimization at the all electron Hartree-Fock level with the STO-3G basis set. The results support the working hypothesis that, like HA, NAGHA monocation approaches the H2-receptor as the N(3)-H tautomer. Neutralization at the anionic site also shifts the preference in tautomeric equilibrium toward the N(1)-H form, thereby triggering the charge relay sequence that was proposed as an activation mechanism of the H2-receptor. The dependence of these mechanisms of interaction with the receptor on the conformation of the side chain as well as on the position at which the negative receptor site interacts with the guanyl group suggests explanations both for the lower affinity and for the partial agonist properties of NAGHA at the H2-receptor.

A guide to two-electron integral approximations through semiorthogonal basis sets

A numerical comparison of the two-electron integrals computed in nonorthogonal STO-3G, semiorthogonal, and orthogonal basis sets is presented. The symmetric orthogonal basis two-electron integrals mimic the zero differential overlap approximation but because of the nonsparse nature of S–1/2 make algorithms for integral approximations impractical. By using a semiorthogonalization scheme which orthogonalizes the weakly overlapping orbital pairs, it is shown that a systematic method for neglecting two-electron integrals can be developed. Applications to semiempirical and nonempirical calculations are discussed.

Ab initio molecular orbital calculations on hydrogen bonding in binary water-alcohol mixtures: (CH3OH)2(H2O), (CH3OH) (H2O)2, and (CF3CH2OH)(H2O)

Ab initio LCAO-SCF molecular orbital calculations have been performed on open-chain and cyclic trimers containing methanol and water and on dimers containing 2,2,2-trifluoroethanoI and water. These calculations were done in conjunction with experimental studies of molecular association in vapors of binary mixtures. Equilibrium structures and energies were determined using the minimal STO-3G basis set. The 2:1 and 1:2 methanol-water cyclic trimers have similar binding energies and are more stable than their respective open-chain trimers. Limited calculations were carried out to assess the importance of polarization functions and correlation energy in the methanol-water trimers. These calculations confirmed the STO-3G predictions. The most stable trifluoroethanol-water dimer has an O—H O and an H F hydrogen bond. It has a larger interaction energy than either a trifluoroethanol dimer or a water dimer.

Comparison between Ab Initio and semiempirical net atomic charges of some nicotinic acetylcholine receptor agonists

We have calculated the net atomic charges and molecular electrostatic potentials of two potent nicotinic acetylcholine receptor agonists, isoarecolone and acetylpiperazine, by three different methods to see how well they correlate and if the simplest method gives the same predictive results. The calculational methods involved calculating net atomic charges by semiempirical (MNDO from MOPAC) and ab initio (Mulliken) and ab initio (potential derived) at STO-3G basis set level. Some deviations were observed when comparisons were made atom by atom, but when group comparisons were made, good correlations were observed. When these partial charges were used to calculate the respective molecular electrostatic potentials on the van der Waals surface, very good correlations were obtained. This study shows that for routine electrostatic calculations, semiempirical MNDO Calculations give similar results and thus lead to similar predictions.

Ab initio calculations on hydrogen bonding in alcohols: Dimers of CH3OH, CH3CH2OH, and CF3CH2OH

Ab initio calculations on a series of alcohol dimers including (CH3OH)2, (CH3CH2OH)2, and (CF3CH2OH)2 have been carried out to compare the effects of various substituents on the hydrogen bond energies and structures and to correlate the results with the wealth of new experimental data on them. Calculations were done with the minimal STO-3G basis set. The methanol and ethanol dimers both have nearly linear hydrogen bonds. The ethanol dimer is also similar in energy to the methanol dimer. Dimers involving both the g-staggered and t-staggered isomers of 2,2,2-trifluoroethanol were considered. The g-staggcred isomer is more stable than the t-staggered isomer by 0.7 kcal/mol and has an intramolecular bond. The dimer of the t-staggered isomer was found to have a linear hydrogen bond as in the methanol and ethanol dimers with a similar hydrogen bond energy. In contrast, the dimer of the g-staggcred isomer has a cyclic structure which is more stable by about 0.5 kcal/mol. The results are consistent with experimental measurements of the gas phase enthalpies of association of alcohols.

Synthesis, chiroptical properties, and their theoretical simulation of some highly rotating benzotricamphor derivatives

The large molecules 1-3 (69, 90, and 102 atoms, respectively), prepared by cyclotrimerization of enantiomerically pure derivatives of (-)-bornyl acetate, show intense ECD spectra, high optical rotation (OR) values (200-1300, in absolute value) dominated in sign and order of magnitude by the lowest-energy Cotton effects, that is, they are the ideal candidates to test the reliability of our "approximate" (TDDFT/B3LYP/6-31G* or smaller basis set) approach to the calculation of chiroptical properties. As a matter of fact, a correct simulation of the OR values and ECD spectra of 1 and 2 can be obtained even using STO-3G basis set and semiempirical or molecular mechanics input geometries: for 1, at the TDDFT/B3LYP/STO-3G level, the OR values are of the order of 500-550, versus an experimental value ranging between 660 and 690, depending on the solvent. On the contrary, the case of 3 (exp. OR between -1330 and -1500) is really complex (for instance, the OR values range between -3216 and -729 (TDDFT/B3LYP/6-31G* calculations) or -1824 and -444 (TDDFT/B3LYP/STO-3G calculations)), making the comparison between calculated and experimental values more difficult. The behavior of 3 is due to its molecular flexibility, whereas 1 is a really rigid molecules and 2 behaves (vide infra) as it were a rigid system. These observations strongly indicate that the conformational freedom constitutes one of the major difficulties for a correct but simple simulation of the chiroptical properties.

Antidiabetic Bis-Maltolato-OxoVanadium(IV): Conversion of inactive trans- to bioactive cis-BMOV for possible binding to target PTP-1B

The postulated transition of Bis-Maltolato-OxoVanadium(IV) (BMOV) from its inactive trans- into its cis-aquo-BMOV isomeric form in solution was simulated by means of computational molecular modeling. The rotational barrier was calculated with DFT - B3LYP under a stepwise optimization protocol with STO-3G, 3-21G, 3-21G*, and 6-31G ab initio basis sets. Our computed results are consistent with reports on the putative molecular mechanism of BMOV triggering the insulin-like cellular response (insulin mimetic) as a potent inhibitor of the protein tyrosine phosphatase-1B (PTP-1B). Initially, trans-BMOV is present in its solid dosage form but in aqueous solution, and during oral administration, it is readily converted into a mixture of "open-type" and "closed-type" complexes of cis-aquo-BMOV under equilibrium conditions. However, in the same measure as the "closed-type" complex binds to the cytosolic PTP-1B, it disappears from solution, and the equilibrium shifts towards the "closed-type" species. In full accordance, the computed binding mode of cis-BMOV is energetically favored over sterically hindered trans-BMOV. In view of our earlier report on prodrug hypothesis of vanadium organic compounds the present results suggest that cis-BMOV is the bioactive species.

Modeling vacancies and hydrogen impurities in graphene: A molecular point of view

We have followed a ‘molecular’ approach to study impurity effects in graphene. This is thought as the limiting case of an infinitely large cluster of benzene rings. Therefore, we study several carbon clusters, with increasing size, from phenalene, including three benzene rings, up to coronene 61, with 61 benzene rings. The impurities considered were a chemisorbed H atom, a vacancy, and a substitutional proton. We performed HF and UHF calculations using the STO-3G basis set. With increasing cluster size in the absence of impurities, we find a decreasing energy gap, here defined as the HOMO–LUMO difference. In the case of H chemisorption or a vacancy, the gap does not decrease appreciably, whereas it is substantially reduced in the case of a substitutional proton. The presence of an impurity invariably induces an increase of the density of states near the HOMO level. We find a zero mode only in the case of a substitutional proton. In agreement with experiments, we find that both the chemisorbed H, the substitutional proton, and the C atom near a vacancy acquire a magnetic moment. The relevance of graphene clusters for the design of novel electronic devices is also discussed.

Photoinduced Intramolecular Charge Transfer in Donor-acceptor Dyad and Donor-bridge-acceptor Triad

The ground and excited state properties of the [60]fullerene, diphenylbenzothiadiazole-triphenylamine (PBTDP-TPA) dyad and fullerene-diphenylbenzothiadiazole-triphenylamine (fullerene-PBTDP-TPA) triad were investigated theoretically using density functional theory with B3LYP functional and 3-21G basis set and time-dependent density functional theory with B3LYP functional and STO-3G basis set as well as 2D and 3D real space analysis methods. The 2D site representation reveals the electron-hole coherence on excitation. The 3D transition density shows the orientation and strength of the transition dipole moment, and the 3D charge difference density gives the orientation and result of the intramolecular charge transfer. Also, photoinduced intermolecular charge transfer (ICT) in PBTDP-TPA-fullerene triad are identified with 2D and 3D representations, which reveals the mechanisms of ICT in donor-bridge-acceptor triad on excitation. Besides that we also found that the direct superexchange ICT from donor to acceptor (tunneling through the bridge) strongly promotes the ICT in the donor-bridge-acceptor triad.

Ab Initio MO-MD Simulation Based on the Fragment MO Method. A Case of (−)-Epicatechin Gallate with STO-3G Basis Set

Abstract We performed ab initio MO-MD simulation based on the fragment MO (FMO) method using the (−)-epicatechin gallate in order to examine the efficiency of fragmentation pattern in comparison with conventional MO-MD. We clearly demonstrated that the FMO-MD simulation gave sufficient results concerning the trajectory of the total energy and the geometry difference.

Ab initio Hartree-Fock calculations on linear and second-order nonlinear optical properties of new acridine-benzothiazolylamine chromophores

The calculation of optimized molecular structure and molecular hyperpolarizability of four new acridine-benzothiazolylamine chromophores (1-4) [2-nitro-6-(piperid-1-yl) acridine (1), 6-(benzothiazol-2-yl-amino)-2-nitro-acridine (2), 6-(6-ethylcarboxylate-benzothiazol-2-yl-amino)-2-nitroacridine (3), 6-(6-(beta-hydroxyethyl-benzothiazol-2-yl-amino)-2-nitroacridine (4)] have been investigated using ab initio methods. Ab initio optimization were performed at the Hartree-Fock level using STO-3G basis set. The first hyperpolarizabilities have been calculated at the Hartree-Fock method with 6-31G and 6-311G basis sets using Gaussian 98W. In general, the first hyperpolarizability is dependent on the choice of method and basis set. To understand this phenomenon in the context of molecular orbital picture, we examined the frontier molecular orbital energies of all the molecules by using HF/6-31G, 6-311G levels. The polarizability, anisotropy of polarizability and ground state dipole moment of all the molecules have also been calculated. These acridine-benzothiazolylamine chromophores display significant second-order molecular nonlinearity, beta (60.2-137.0 x 10(-30) esu) and provide the basis for future design of efficient nonlinear optical materials having the acridine-benzothiazolylamine core.

Study on the potential energy function for the ground state （X1Σ+）of SiO molecule by density functional theory

The structural optimization for the ground state (X1Σ+) of SiO molecule has been calculated using density functional theory B3P86 method with the basis sets STO-3G, D95**, 6-311G, 6-311++G, 6-311++G** and cc-PVTZ. The conclusion is draun by comparison that the basis set cc-PVTZ is the most suitable for the structural optimization calculation of the ground state (X1Σ+) of SiO molecule. The analytical potential energy curve for the ground state (X1Σ+) of SiO molecule is scanned using B3P86/cc-PVTZ method, and then fitted to the Murrell-Sorbie function using least squares. At last the spectroscopy constants (Be，αe，ωe and ωeχe) related to the analytical potential energy function are calculated and compared with the experimental data.

Reactivity of tourmaline by quantum chemical calculations

ZnAb initio calculations on reactivity of tourmaline were performed using both Gaussian and density function theory discrete variation method (DFT-DVM). The HF, B3LYP methods and basis sets STO-3G(3d,3p),6-31G(3d,3p) and 6-311++G(3df,3pd) were used in the calculations. The experimental results show energy value obtained from B3LYP and 6-31++1G(3df,3pd) basis sets is more accurate than those from other methods. The highest occupied molecular orbital (HOMO) of the tourmaline cluster mainly consists of O atom of hydroxyl group with relative higher energy level, suggesting that chemical bond between those of electron acceptor and this site may readily form, indicating the higher reactivity of hydroxyl group. The lowest unoccupied molecular orbital (LUMO) of the tourmaline cluster are dominantly composed of Si, O of tetrahedron and Na with relative lower energy level, suggesting that these atoms may tend to form chemical bond with those of electron donor. The results also prove that the O atoms of the tourmaline cluster have stronger reactivity than other atoms.