MNDO Method Research Articles

Enthalpy of formation of adamantane alkyl derivatives

The enthalpies of formation of adamantane alkyl derivatives were calculated by the semiempirical quantum chemical methods PM3, MINDO, AM1 and MNDO of the MOPAC software package. Comparison of the calculated values with the experimental data showed that the best correlation gave the PM3 method. Using this method and linear regression equation derived by us we calculated enthalpies of formation of twenty-two alkyl derivatives of adamantane.

The consistency analysis of different semiempirical calculations on second- and third-order nonlinear optical properties of donor–acceptor chromophores containing α-cyan

The static and frequency dependent average polarizability (< α>), first- and second-hyperpolarizabilities (< β> and < γ>) and HOMO and LUMO energies of donor–acceptor chromophores containing α-cyan ( 1a– c) have been investigated by using the AM1, MNDO, MNDO-d, PM3, RM1 and PM6 methods within a time-dependent Hartree–Fock (TDHF) approaches. The electronic properties of 1a– c have been reported by employing two-state model calculated at ZINDO/S-SCI, PM3-SCI and RM1-SCI methods. Also, the molecular hardness ( η) and electronegativity ( χ) parameters have been obtained by using molecular frontier orbital energies. The < α>, < β>, < γ> HOMO, LUMO energies, η and χ parameters have been investigated with respect to the choice of different semiempirical methods. The variation graphics of β, β 0, η and χ parameters according to the different semiempirical methods are presented. Furthermore, the variation graphics of β 0 with regard to the μ eg , Δ μ and λ eg are displayed. The frontier molecular orbital and electrostatic potential pictures of 1a– c using ZINDO/S-SCI level have been examined. The results of 1a– c display significant second- and third-order molecular nonlinearity.

Quantum Chemical Calculation of the Monoaminocarbonic Acids

For the first time quantum chemical MNDO method has been used for the calculation of a classical row of monoaminocarbonic acids of glycines, α-alanines, β-alanines, valines, isoleucines, norvalines and γ–aminobutyric acids, leucines and phenylalanines. The optimized geometrical and electronic structure of these compounds has been received.

Removal of Methyl Tert-Butyl Ether from Air-Groundwater in Environment by Carbon Nanotube: Ab Initio Studies

ABSTRACT Gasoline and heating oil travel through pipelines and are also distributed by truck to above-ground and underground storage tanks. Through its extensive use as a fuel oxygenate, methyl tert-butyl ether (MTBE) is found nearly ubiquitously throughout the environment. MTBE, a widely used gasoline additive, is recently being scrutinized for potential environmental damage in groundwater and in the atmosphere. We study the structural, total energy, thermodynamic, and conductive properties of absorption of MTBE on carbon nanotube (CNT), which converts to CO and H2O. There are four situations for MTBE to be near by single-walled nanotube (SWNT) that we have investigated its adsorption on CNT and convertion to other products. The thermodynamic properties are calculated for them. The calculations have quantum mechanical detail and are based on a semiempirical (MNDO method), which is applied to the evaluation of both the electronic structure and of the conductance.

Sensor Response to Alcohol and Chemical Mechanism of Carbon Nanotube Gas Sensors

The reaction of ethanol and methanol over carbon nanotubes (CNTs) has been investigated. The main reaction product in all cases is acetaldehyde and formaldehyde, with secondary products such as ethyl acetate and methyl format. CNTs have many distinct properties that may be exploited to develop the next generation of sensors. We study the distinct physical, electronic, and mechanical properties of CNTs. This artivcle aims to act as a reference source for researchers to help them in developing new applications of CNT‐based sensors. Interaction between alcohol molecules and CNT is investigated using a semi‐empirical MNDO method. We study the total energy, electron, and thermodynamic properties adsorption alcohols on armchair single‐walled carbon nanotubes (SWNT (4,4)) obtained at room temperature. In this study presented a comprehensive studying on effects of gases on SWNT that it is on its electronic structure and transfer of charge from the atoms to the SWNT. The ethanol and methanol converted to other oxidation products on SWNT‐based sensors.

Averaging Semiempirical NMR Chemical Shifts: Dynamic Effects on the Subpicosecond Time Scale

The variation of the (1)H and (13)C NMR chemical shifts of heptapeptide ATWLPPR was investigated during a hybrid quantum mechanical (QM)/molecular mechanical (MM = CHARMM) molecular dynamics simulation of the peptide in aqueous solvent. The semiempirical method OM3 was used as the QM method, and the effect of augmenting the OM3 Hamiltonian with an empirical dispersion term (OM3-D) was also explored. The semiempirical MNDO method was used to calculate the chemical shifts of snapshots taken at 50 fs intervals during the 100 ps simulation. The calculated chemical shifts are highly sensitive to fluctuations of the molecular geometry on the time scale of molecular vibrations. However, the time-averaged chemical shift over the full simulation results in reasonable agreement with the experimental NMR chemical shifts and more consistent results compared with the averaged chemical shifts obtained from gas-phase optimized conformations of the peptide. The OM3 and OM3-D methods are stable and reproduce the main features of the experimental geometry during the 100 ps simulation.

A theoretical investigation of the first step in the metabolic reduction of halogenated methanes by cytochrome P-450

The first step in the anaerobic reduction of halogenated hydrocarbons by cytochrome P–450 is the Abstraction of an electron from the reduced enzyme by the substrate located in a lipophilic binding site. To determine which halogenated hydrocarbons might be active substrates for this reductive metabolism, the vertical electron affinity of a number of bromo- and iodohalomethanes has been calculated using the MNDO method. Combining these results with earlier calculations on the fluoro- and chlorohalomethanes, and examining the available experimental evidence, yields the prediction that among the chloro- and fluoromethanes, only CF2Cl2, CHCl3, CFCl3, and CCl4 could be active substrates. Similarly, all bromohalomethanes, with the exception of CH3Br, CH2FBr, and CHF2Br, are predicted to be active substrates, as are all iodohalomethanes, including CH3I.

Influence of defects in the carbon network on the static polarizability of fullerenes

The static polarizability of the C60, C70, C80, and C186 fullerenes has been calculated within the semiempirical MNDO approximation implemented in the MOPAC quantum-chemical program package. It is demonstrated that the results obtained are comparable with experimental data and the results of the ab initio B3LYP method using the 6–31G(d, p) basis set. The influence of topological defects (five-, seven-, and eight-membered rings), vacancies produced by removing pentagons, and nitrogen and boron atoms on the geometric parameters and the polarizability of the C60, C240, and C540 fullerenes has been investigated by the MNDO method. It is revealed that the polarizability of the fullerene with topological defects is higher than the polarizability of the perfect icosahedral fullerene. The formation of vacancies in the carbon cage leads to a linear decrease in the polarizability of the fullerene and an increase in the specific polarizability. The polarizability of the heterofullerene with nitrogen or boron atoms spaced apart in the carbon cage is higher than that of the fullerene with heteroatoms located adjacent to each other.

Partial Charge Calculation Method Affects CoMFA QSAR Prediction Accuracy

The 3D-QSAR method comparative molecular field analysis (CoMFA) involves the estimation of atomic partial charges as part of the process of calculating molecular electrostatic fields. Using 30 data sets from the literature the effect of using different common partial charge calculation methods on the predictivity (cross-validated R2) of CoMFA was studied. The partial charge methods ranged from the popular Gasteiger and the newer MMFF94 electronegativity equalization methods, to the more complex and computationally expensive semiempirical charges AM1, MNDO, and PM3. The MMFF94 and semiempirical MNDO, AM1, and PM3 methods for computing charges were found to result in statistically significantly more predictive CoMFA models than the Gasteiger charges. Although there was a trend toward the semiempirical charges performing better than the MMFF94 charges, the difference was not statistically significant. Thus, semiempirical partial charge calculation methods are suggested for the most predictive CoMFA models, but the MMFF94 charge calculation method is a very good alternative if semiempirical methods are not available or faster calculation speed is important.

Calculations of the enthalpies of formation of oxygen-containing adamantane derivatives by quantum-chemical methods

The enthalpies of formation of oxygen-containing adamantane derivatives were calculated using the semiempirical quantum-chemical PM3, MINDO, AM1, and MNDO methods implemented in the MOPAC package. The calculated and experimental values were compared. The best correlation was obtained for AM1 calculations. This method was therefore used to calculate the enthalpies of formation of 20 oxygen-containing adamantane derivatives.

QM–MM interactions in simulations of liquid water using combined semi-empirical/classical Hamiltonians

Well-established semi-empirical quantum-mechanical methods such as AM1, PM3 and MNDO poorly describe hydrogen-bonding interactions. The recently developed OM1, OM2 and OM3 methods, which include explicit corrections in the one-electron terms of the Hamiltonian to counteract for the neglect of orthogonalization effects, show an improved description of hydrogen bonding. In the current work we compare the performance of the OMx models on the one hand and the AM1, PM3 and MNDO methods (as well as the SCC-DFTB method) on the other when used in combination with a classical force field in QM/MM calculations on a water dimer in the gas phase, and in QM/MM simulations of a QM water 'solute' in liquid MM water. It is found that when using the OMx methods to describe the QM water molecule, values for QM-MM interaction energies and the molecular dipole moment of the QM solute are significantly closer to experiment than when using the other semi-empirical methods. In addition, the compatibility of OM3 with the classical Hamiltonian improves upon explicitly including electronic polarization in the MM subsystem.

Dynamic NMR study of the oxaphosphetane complexation with lithium during the Wittig reaction

AbstractDynamic NMR spectroscopy at very low temperatures (148–182 K) reveal the dynamic behavior of the (2‐tri(3‐furyl)‐3‐methyl‐4‐cyclopropenyl‐oxaphosphetane) generated during a Wittig reaction between tri(3‐furyl)ethylphosphonium iodine and cyclopropylaldehyde. The possibility of formation of different adducts between Li+ ions and oxaphosphetane or betainic intermediates was checked calculating the formation enthalpies using the MNDO, AM1, and PM3 semiempirical MO methods. The observed species are interpreted as oxaphosphetane complexes with lithium ions present in solution. Quantum mechanical calculations confirm the spectroscopic results. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008

Clustering of molecular hydrogen anion [formula omitted] on a [formula omitted] surface

The structures and binding energies of H 3 - anions clustering on a Li + @ C 60 surface have been studied using MNDO method. The calculations indicate that the metallofullerene Li + @ C 60 , which has a high hydrogen capacity of 9 wt% with a binding energy of 0.05 eV/ H 2 , could be practical for hydrogen storage at reduced temperatures, when introducing H 3 - anions clustering on the surface.

Performance of the semiempirical AM1, PM3, MNDO, and tight-binding methods in comparison with DFT method for the large fullerenes C 116–C 120

Are the semiempirical methods still reliable for large fullerenes? To answer this question, in this paper, the semiempirical AM1, PM3, MNDO, and tight-binding calculations were performed on the candidate isomers selected from the complete sets of isolated-pentagon-rule isomers of C 116–C 120 based on the second generation reactive empirical bond order potential. To assess the reliability of these semiempirical methods and predict the ground-state structures more accurately, the density functional theory calculations at the B3LYP/6-31G(d)//B3LYP/3-21G level of theory were also carried out on the top 20 low-energy candidates from each semiempirical method. It was found that the tight-binding potential gives a good agreement for the prediction of the relative energies when compared with the B3LYP/6-31G ∗ results, while AM1, PM3, and MNDO methods behave badly. Furthermore, we also investigated the structures of the B3LYP/6-31G ∗ low-energy isomers for C 116–C 120 to understand the relationship between the stability and some structural factors.

Conformational analysis for some nonclassical antagonists of histamine H3 receptor

AbstractA conformational search in vacuum for a series of 1,3‐substituted pyrrolidine derivatives has been performed using the AMBER, AM1, PM3, and MNDO methods. Conformational analysis of the pyrrolidine ligands suggests that these compounds could have many conformers that populate the low‐energy minima on the potential energy surface (PES). The conformational space occupied by the ligands is large and, in vacuum, the rotation barriers of different flexible bonds have energies between 0.5 and thousands of kcal/mol. By optimization, most conformers have energy barriers of 0–5 kcal/mol; thus, they could interconvert easily to obtain better interactions in the receptor active site. Optimized conformers having energy barriers of &gt;5 kcal/mol display bad geometries with very large bond lengths and deformed rings. Shapes and heights of rotation barriers obtained through COSMO–AM1 single‐point calculations in water are similar to those obtained from single‐point calculations in vacuum. However, in water the energy barriers are lower, allowing most conformers to convert in other low‐energy conformers. The best conformers in vacuum and in water are different: the gas phase best conformer has a helical shape, while the best conformer in water has an extended shape. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007

Quantum-chemical calculations of the piezoelectric characteristics of boron nitride and carbon nanotubes

The piezoelectric characteristics of boron-nitride and carbon nanotubes were calculated. The electronic structure of nanotubes was studied using the quantum-chemical semiempirical MNDO method within a molecular-cluster model. The piezoelectric constants e zzz, e xzz, and e xxx of boron nitride nanotubes of two structural modifications (n, n) (n = 5, 6, ..., 9) and (n, 0) (n = 6, 7, ..., 12) were calculated. The values of the piezoelectric constants e zzz of tubular boron nitride are found to be close in order of magnitude to the respective values obtained using nonempirical calculation methods. The piezoelectric constant e xzz of a (6, 6) carbon nanotube doped with substitutional point defects was calculated.

Quantitative structure–activity relationships for prediction of the toxicity of hydroxylated and quinoid PCB metabolites

Quantitative structure-activity relationship (QSAR) models were developed for the in vitro potencies to downregulate gap junctional intercellular communication (GJIC) of hydroxylated polychlorinated biphenyls (OH-PCBs) and PCB quinines using partial least squares (PLS) regression. Quantum chemical descriptors computed by the semiempirical AM1, PM3 and MNDO methods were used as predictor variables. The cross-validated Q2cum values for the three optimal QSAR models are 0.784, 0.789 and 0.755, respectively, indicating good predictive capabilities for the acute inhibition of GJIC (IC(50)) of oxygenated PCB derivatives. The slightly higher Q2cum value of the model using computed molecular descriptors from the PM3 Hamiltonian suggested a slightly better predictive power than the models developed using AM1 or MNDO. However, given these dispersion parameters in these three optimal models, there would not be a significant difference between the Q2cum values. Results from this study showed that the logarithmic scale of IC(50) is affected by different molecular structural descriptors.

Investigating the molecular formation properties of ethyl 4-(2-oxobenzothiazolin-3-yl) butanoate using PM3, AM1, MNDO methods

Investigating the molecular formation properties of ethyl 4-(2-oxobenzothiazolin-3-yl) butanoate using PM3, AM1, MNDO methods

Assessment of semiempirical methods for the computation of charge transfer in DNA π-stacks

Using CAS-PT2 and CASSCF charge transfer (CT) energies and electronic couplings as reference data, we assess the performance of several semiempirical methods in the calculation of hole transfer in π-stacks of nucleobases. INDO/S is the most reliable of the methods examined. It provides very good estimates for the key CT parameters. While the MNDO, AM1 and PM3 methods give reasonable CT energies, they fail to provide acceptable values of the coupling matrix elements in the stacks.

NO-MNDO: Reintroduction of the Overlap Matrix into MNDO.

The effect of reintroducing the overlap matrix into the secular equations for an NDDO (neglect of diatomic differential overlap)-based semiempirical molecular orbital method has been investigated. The modification is expected to improve the description of interactions between electron pairs. The idea has been tested by implementation and evaluation of a nonorthogonal version of the MNDO method (NO-MNDO) with parametrization for hydrogen, carbon, nitrogen, and oxygen. Overall, the accuracy of NO-MNDO for heats of formation is nearly identical to that for the more highly parametrized AM1 method. The mean absolute error (MAE) for heats of formation of a comprehensive set of 622 neutral, closed-shell molecules is reduced from 8.4 kcal/mol with MNDO to 6.8 kcal/mol with NO-MNDO. In addition, the performance for conformational equilibria and torsional barriers is significantly improved with NO-MNDO, presumably owing to the improved description of closed-shell interactions. For molecular geometries, the usual training and test sets have been expanded through use of MP2/6-31G(d) results for consistent comparisons. The performance of NO-MNDO for bond lengths, bond angles, and dihedral angles remains good with MAEs of 0.017 Å, 2.5°, and 4.5°. Additionally, NO-MNDO corrects severe errors by MNDO for R(•) + H-R' hydrogen-atom transfers, while testing for activation barriers for nine pericyclic reactions reveals only modest improvement.