MNDO Hamiltonian Research Articles

Theoretical and experimental studies on the corrosion inhibition potentials of some purines for aluminum in 0.1 M HCl

Experimental aspect of the corrosion inhibition potential of adenine (AD), guanine (GU) and, hypoxanthine (HYP) was carried out using weight loss, potentiodynamic polarization and electrochemical impedance spectroscopy (EIS) methods while the theoretical aspect of the work was carried out by calculations of semi-empirical parameters (for AM1, MNDO, CNDO, PM3 and RM1 Hamiltonians), Fukui functions and inhibitor–metal interaction energies. Results obtained from the experimental studies were in good agreement and indicated that adenine (AD), guanine (GU) and hypoxanthine (HYP) are good adsorption inhibitors for the corrosion of aluminum in solutions of HCl. Data obtained from electrochemical experiment revealed that the studied purines functioned by adsorption on the aluminum/HCl interface and inhibited the cathodic half reaction to a greater extent and anodic half reaction to a lesser extent. The adsorption of the purines on the metal surface was found to be exothermic and spontaneous. Deviation of the adsorption characteristics of the studied purines from the Langmuir adsorption model was compensated by the fitness of Flory Huggins and El Awardy et al. adsorption models. Quantum chemical studies revealed that the experimental inhibition efficiencies of the studied purines are functions of some quantum chemical parameters including total energy of the molecules (TE), energy gap (EL–H), electronic energy of the molecule (EE), dipole moment and core–core repulsion energy (CCR). Fukui functions analysis through DFT and MP2 theories indicated slight complications and unphysical results. However, results obtained from calculated Huckel charges, molecular orbital and interaction energies, the adsorption of the inhibitors proceeded through the imine nitrogen (N5) in GU, emanine nitrogen (N7) in AD and the pyridine nitrogen (N5) in HPY.

Semiempirical Quantum Chemical Calculations Accelerated on a Hybrid Multicore CPU-GPU Computing Platform.

In this work, we demonstrate that semiempirical quantum chemical calculations can be accelerated significantly by leveraging the graphics processing unit (GPU) as a coprocessor on a hybrid multicore CPU-GPU computing platform. Semiempirical calculations using the MNDO, AM1, PM3, OM1, OM2, and OM3 model Hamiltonians were systematically profiled for three types of test systems (fullerenes, water clusters, and solvated crambin) to identify the most time-consuming sections of the code. The corresponding routines were ported to the GPU and optimized employing both existing library functions and a GPU kernel that carries out a sequence of noniterative Jacobi transformations during pseudodiagonalization. The overall computation times for single-point energy calculations and geometry optimizations of large molecules were reduced by one order of magnitude for all methods, as compared to runs on a single CPU core.

Convergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations

Lately, there has been great interest in performing free-energy perturbation (FEP) at the combined quantum mechanics and molecular mechanics (QM/MM) level, e.g. for enzyme reactions. Such calculations require extensive sampling of phase space, which typically is prohibitive with density-functional theory or ab initio methods. Therefore, such calculations have mostly been performed with semiempirical QM (SQM) methods, or by using a thermodynamic cycle involving sampling at the MM level and perturbations between the MM and QM/MM levels of theory. However, the latter perturbations typically have convergence problems, unless the QM system is kept fixed during the simulations, because the MM and QM/MM descriptions of the internal degrees of freedom inside the QM system are too dissimilar. We have studied whether the convergence of the MM → QM/MM perturbation can be improved by using a thoroughly parameterised force field or by using SQM/MM methods. As a test case we use the first half-reaction of haloalkane dehalogenase and the QM calculations are performed with the PBE, B3LYP, and TPSSH density-functional methods. We show that the convergence can be improved with a tailored force field, but only locally around the parameterised state. Simulations based on SQM/MM methods using the MNDO, AM1, PM3, RM1, PDDG-MNDO, and PDDG-PM3 Hamiltonians have slightly better convergence properties, but very long simulations are still needed (~10 ns) and convergence is obtained only if electrostatic interactions between the QM system and the surroundings are ignored. This casts some doubts on the common practice to base QM/MM FEPs on semiempirical simulations without any reweighting of the trajectories.

ChemInform Abstract: Semiempirical Calculations of Hyperpolarizabilities for Donor-Acceptor Molecules: Comparison to Experiment

The dipole moments (μ), polarizabilities (α), hyperpolarizabilities (β), and second-order hyperpolarizabilities (γ) of benzene, biphenyls, fluorene, styrene, stilbenes, and tolans have been calculated by a finite field method with the PM-3 parametrization of the MNDO Hamiltonian. These results were compared to experimental value obtained from EFISH and THG measurements. Good correlations were obtained, and coefficients between the measured and calculated value (calculated/measured) were 1.11, 0.75, 1.00, and 0.94 for μ, α, β, and γ, respectively

DIADORIM: a Monte Carlo Program for liquid simulations including quantum mechanics and molecular mechanics (QM/MM) facilities: applications to liquid ethanol

This paper presents a Metropolis Monte Carlo (MMC) computer program developed to simulate liquids and solutions including QM/MM facilities: the energy from intermolecular interactions is calculated with classical force field functions and the internal molecular energies are calculated using Quantum Chemistry methods. The following facilities were implemented: (i) the semiempirical MOPAC 6 quantum chemistry package was included as a subroutine of the main MMC simulation program; (ii) alternatively, an interface with an external data bank was developed to allow the use of energies previously obtained; (iii) calculation in NpT and NVT ensembles are available; (iv) the trajectory generated along the MMC sampling can be saved using standard xtc file format allowing trajectory visualization and data analysis using external programs. The program was used to calculate thermodynamical and structural properties of liquids ethanol (ET) in the NpT ensemble at 1.0 atm and 298 K. Bond angles and bond distances of ethanol molecules were kept constant but torsions along the dihedral angle defined by the H-O-C-C atoms were sampled in the simulation. QM/MM calculations were performed using the MOPAC AM1, PM3 and MNDO Hamiltonians to calculate the internal molecular energy. Calculations using internal energies obtained with OPLS-AA force field, ab initio HF/6-31g*, MP2/6-31g* and B3LYP/6-31g* calculations were performed. The dihedral angles distributions obtained with different methodologies reveal extraordinary qualitative and quantitative differences. However, the pair energies and radial distributions functions obtained with the different methodologies are in good agreement. The values calculated for the density and enthalpy of vaporization of liquid ethanol are in good agreement with experimental data.

Theoretical Study of the Kinetics of the Pyrolytic Elimination Reaction of Ethyl Chloride

The products of the gas‐phase elimination of ethyl chloride are hydrogen chloride and ethane. Using AM1, MNDO and PM3 Hamiltonians of quantum mechanical computer code called MOPAC, a procedure for the kinetics and computation of the Arrhenius parameters for the pyrolytic elimination reaction of ethyl chloride was devised in order to evaluate the predictive ability of the three Hamiltonians used. The first‐order rate coefficient for the three Hamiltonians are 1.15x10-8s-1, 4.55x10-15s-1 and 5.36x10-4s-1 for AM1, MNDO and PM3 respectively. The results obtained showed that the rate constant for the computed Arrhenius parameters compare well with the experimental values in the literature, thus showing that the computational procedure adequately simulates experimental results; also the semi‐empirical AMI calculation has the best predictive ability with experiment followed by PM3 while MNDO has the least.

Validation of Linear Scaling Semiempirical LocalSCF Method.

The numerical accuracy of linear scaling semiempirical methods LocalSCF and MOZYME is analyzed in comparison to conventional matrix diagonalization with respect to a variety of molecular properties including conformational energy, dipole moment, atomic charges, and bond orders. Major semiempirical MNDO, AM1, PM3, and PM5 Hamiltonians were considered in the study. As the numerical tests demonstrate, both LocalSCF and MOZYME reasonably reproduce matrix diagonalization results with the deviations being below the accuracy of semiempirical methods. However, the economical LocalSCF memory consumption and faster calculations are more beneficial for the quantum-mechanical modeling of large biological systems. The computational performance of the LocalSCF method is tested on the conformational energy calculation of a series of molecular dynamics snapshots of insulin in a large box of water.

Theoretical and experimental study of optical second harmonic generation in new chiral thiolates salts

The second harmonic generation ability of new chiral thiolate salts is investigated. Aromatic thiolate anions ArS − are expected from semi-empirical calculations with PM3 parameterization of the MNDO Hamiltonian to possess higher intrinsic polarizabilities than the parent neutral thiols ArSH. Salts associating (hyper)polarizable aromatic thiolate anions with chiral cations, which ensure the noncentrosymmetry necessary to have second-order nonlinear optical effects have been synthesized. The first hyperpolarizabilities, β, of the salts are measured using hyper-Rayleigh scattering technique. Second harmonic generation powder tests (Kurtz and Perry method) carried out on various salts studied, were positive indicating that these materials crystallize in noncentrosymmetric space groups.

Linear free energy relationships on rate constants for dechlorination by zero-valent iron

By correlation analysis, molecular structural factors governing surface area-normalized rate constants ( k ¥ ) for dechlorination by zero-valent iron, were identified. Twenty-nine quantum chemical descriptors computed by MNDO, AM1 and PM3 Hamiltonians for gas-phase and the conductor-like screening model (COSMO) for incorporating solvent (H 2 O) effects were studied. Besides the energy of the lowest unoccupied molecular orbital ( E LUMO ), the character of carbon-chlorine bonds (C-Cl bonds) and especially the strength of C-Cl bonds was found significant in governing the magnitude of log k ¥ . By PLS analysis, six two-parameter linear free energy relationships (LFER) were obtained. The best two-parameter LFER model was the one using E LUMO and C (the Coulombic interaction energy of the two-center term for the C-Cl bonds) computed by PM3/H 2 O method as molecular structural descriptors. Chlorinated compounds with high E LUMO and C values tend to have low dechlorination rate constants.

Semiempirical molecular orbital calculation of azobenzene: stability study of isomers and mechanism of E/Z isomerization

Semiempirical SCF-MO calculations are used to investigate the stability of isomers as well as the mechanism of E/Z isomerization of azobenzenes (1–6). MNDO and PM3 hamiltonians have shown the E isomer to be the most stable, in agreement with the experimental results. AM1, such as CNDO calculation, shows the Z isomer being more stable than the E isomer. This is contrary to all the experimental evidences. The isomerization pathway for interconversion between isomers of each compound is found to be through nitrogen inversion rather than N–N double bond rotation. This agrees well with the experimental mechanism suggested in n-hexane and gas phase. The calculated energy barrier for this process ranges from 20.4 to 31.5kcal/mol.

Nonlinear optical properties of chiral thiolates

Aromatic thiolate anions ArS − are expected from a semi-empirical calculation with PM3 parametrisation of the MNDO Hamiltonian, to possess higher intrinsic polarizabilities than the parent neutral thiols ArSH. Noncentrosymmetric thiolate salts have been synthesized by the reaction of ArSH with chiral amines and investigated for their second-order (through frequency doubling) and third-order (through degenerate four-wave mixing technique) nonlinear optical properties.

Rapid single- and multiple-scattering EXAFS Debye-Waller factor calculations on active sites of metalloproteins.

This paper describes recent results using our approach to calculating self-consistently single (SS) and multiple-scattering (MS) DebyeWaller factors (DWF) on active sites of metalloproteins. The calculation of MS DWF, together with the Feff7 program allows us to simulate ab-initio EXAFS spectra for a given temperature systems with no adjustable parameters. In our latest report (Dimakis N., and Bunker G., 1998) we calculate, using density functional and semiempirical approaches, the SS and MS DWF for small molecules and compared them to Raman, infrared and EXAFS spectra. In this report calculation of DWFs is done for tetrahedral Zn imidazole, a complex containing thirty two atoms that is similar in certain respects to active sites of many metalloproteins. Ab-initio calculation, although it is a more accurate and reliable scheme, it is not at present practical on desktop computers; computation times are weeks. Therefore as an alternative we have tried the semiempirical MNDO Hamiltonian, which is at least three orders of magnitude faster than ab-initio, and can be expected to be of reasonable accuracy because it is parameterized for organic compounds. Our approaches take advantage of commercially available molecular orbital programs. We have written additional programs which, using normal mode calculations, calculate the MS paths, and transparently interface with Fef-f'/to produce the EXAFS spectra. Results are in very good agreement with experimental data tested.

Universal Quantum Mechanical Model for Solvation Free Energies Based on Gas-Phase Geometries

We present a new solvation model for predicting free energies of transfer of organic solutes from the gas phase to aqueous and organic solvents. The model is based on class II charges, gas-phase geometries, a generalized Born approximation to the polarization free energy, and SM5-type atomic surface tensions. The initial parametrization of the new model was developed to utilize the MNDO/d Hamiltonian, and we also present parameters for the MNDO, AM1, and PM3 Hamiltonians. These parametrizations are based on reasonably accurate gas-phase geometries for 43 ions and 260 neutral solute molecules composed of H, C, N, O, F, S, Cl, Br, and I and containing a wide variety of functional groups. For aqueous solutions, the parametrization is based on data for 248 of the neutrals and all of the ions. For organic solvents, it is based on 1836 experimental data points for 227 of the neutral solutes in 90 organic solvents. The parametrization based on the MNDO/d Hamiltonian is called SM5.2R/MNDO/d, and it yields a mean ...

Reparametrizing MNDO for Excited-State Calculations by Using ab Initio Effective Hamiltonian Theory: Application to the 2,4-Pentadien-1-iminium Cation

The ab initio effective valence shell Hamiltonian (ℋ ν) theory is employed to reparametrize the standard MNDO Hamiltonian for MNDO-πCI (configuration interaction) excited-state calculations for the small, protonated Schiff base 2,4-pentadien-1-iminium. The revised parametrization, called differs from the ground-state parametrization via adjustment of the basic p-orbital parameters: UC, UN, βC, GC,C, GN,N. The βC resonance integral is adjusted to remove all electron−electron correlation from the MNDO one-electron, two-center Hu,v π-electron integrals. Likewise, a small correction of 0.25 eV is appended to both UC and UN. The MNDO ground-state GC,C and GN,N π-electron one-center, two-electron repulsion integrals are increased in value by about 1.5 and 2 eV, respectively, to reproduce the average of the ab initio ℋ ν one-center, two-electron effective integrals. Subsequent calculations reproduce the lowest-lying ab initio ℋ ν 20 vertical excitation energies to less than 0.2 eV on average (when full πCI is e...

Using theoretical descriptions in quantitative structure activity relationships: Application to partition properties of alkyl (1-phenylsulfonyl)cycloalkane-carboxylates

The widespread application of computational techniques to studies in biology, chemistry and environmental sciences has led to a quest for important, characteristic molecular parameters that may be directly derived from these computational methods. Theoretical linear solvation energy relationships (TLSER) combine computational molecular orbital parameters with the linear solvation energy relationship (LSER) of Kamlet and Taft to characterize, understand, and protect biological, chemical, and physical properties of chemical compounds. This paper describes the derivation ofTLSERs for three properties, octanol/water partition coefficient, water solubility, and soil adsorption coefficient, for a series of 28 alklyl (1-phenylsulfonyl)cycloalkane-carboxylates. TLSER molecular parameters obtained with both the MNDO and AM1 Hamiltonians are compared, furthermore, these are compared with TLSER descriptions recently proposed by other researchers.

Coulomb screening and exciton binding energies in conjugated polymers

Hartree–Fock solutions of the Pariser–Parr–Pople and MNDO Hamiltonians are shown to give reasonable predictions for the ionization potentials and electron affinities of gas-phase polyenes. However, the energy predicted for formation of a free electron-hole pair on an isolated chain of polyacetylene is much larger than that seen in the solid state. The prediction is 6.2 eV if soliton formation is ignored and about 4.7 eV if soliton formation is included. The effects of interchain interactions on the exciton binding energy are then explored using a model system consisting of one solute and one solvent polyene, that are coplanar and separated by 4 Å. The lowering of the exciton binding energy is calculated by comparing the solvation energy of the exciton state to that of a single hole (a cationic solute polyene) and a single electron (an anionic solute polyene). It is argued that when the relative timescales of charge fluctuations on the solute and solvent chains are taken into account, it is difficult to rationalize the electron–electron screening implicit in the parametrization of a single-chain Hamiltonian to solid-state data. Instead, an electron–hole screening model is developed that includes the time scales of both the electron–hole motion and the solvent polarization. The predicted solvation energies, which are saturated with respect to solute and solvent chain length, are 0.07 eV for the exciton and 0.50 eV for a well separated electron–hole pair. Given this large, 0.43 eV reduction in the exciton binding energy due to interaction with a single chain, it seems likely that interchain interactions play a central role in establishing the solid-state exciton binding energy.

Alternant boron nitride cages: A theoretical study

Heteroatomic cages (BN/2NN/2) with borons and nitrogens fully replacing alternant sets of carbons in cages are built graph-theoretically and investigated via the semiempirical MNDO Hamiltonian. The comparison with their parent carbon cages CN is made in terms both of electronic and of geometric changes. Infinite classes first of octahedral symmetry and second of hexagonal-bipyramidal symmetry fullerenoid cages are considered in detail. The difference in the electronegativities for boron and nitrogen implies the opening of HOMO-LUMO gaps for alternant BN clusters. In general, the borons prefer planar geometry (sp2 hybridization) while the nitrogens prefer pyramidalization (sp3 hybridization). © 1997 John Wiley & Sons, Inc.

A semiempirical scaled force field for simple short-chain phosphazenes Cl 3PN(PCl 2N) n−1 P(O)Cl 2 ( n = 1 and 2)

The present paper reports a set of force constants calculated with a MNDO hamiltonian and scaled using a non-linear optimization procedure to reproduce the observed vibrational frequencies of simple short-chain phosphazenes. The results support the presence of a lower energy conformer of OP(Cl) 2NP(Cl) 3. Normal coordinate analysis of OP(Cl) 2NP(Cl) 2NP(Cl) 3 was also carried out. Conformations, bonding and flexibility are discussed in terms of force field and vibrational frequencies.

Semiempirical MNDO, AM1, and PM3 direct dynamics trajectory studies of formaldehyde unimolecular dissociation

Direct dynamics calculations are performed, using the semiempirical neglect of diatomic differential overlap (NDDO) molecular orbital theory, to explore the level of electronic structure theory required to accurately describe the product energy partitioning when formaldehyde dissociates into hydrogen and carbon monoxide. Trajectories are initiated at the saddlepoint and are propagated for the short time needed to form products, by obtaining the energy and gradient directly from the NDDO theory. The resulting product energy partitioning is compared to available experimental data and the findings of two previous trajectory studies, including one ab initio trajectory study at the HF/6-31G** level of theory [Chem. Phys. Lett. 228, 436 (1994)]. The MNDO, AM1, and PM3 semiempirical Hamiltonians are studied, as well as Hamiltonians based on specific reaction parameters (SRP). For the latter, the original PM3 and AM1 parameters are adjusted to reproduce some ab initio potential energy surface properties, such as stationary points and part of the reaction path. A series of NDDO-SRP Hamiltonians are chosen by fitting different features of a HF/6-31G** potential energy surface. Only qualitative agreement is found between the product energy distributions of the NDDO-SRP Hamiltonians and that of the HF/6-31G** Hamiltonian. This result is consistent with the well known difficulty of reproducing a HF/6-31G** Hamiltonian with a NDDO-SRP model, since dynamic correlation is not treated in ab initio SCF, but is incorporated into semiempirical methods. Trajectory results with NDDO-SRP Hamiltonians, which reproduce a few experimental and/or high-level ab initio stationary points, are in poor agreement with the experimental product energy partitioning. Reparameterizing the NDDO Hamiltonian is laborious, and only a few properties of the potential energy surface can be reproduced at the same time. This indicates the limitations of the NDDO-SRP approach, which might be well suited for locally interpolating ab initio data, but not for quantitatively describing global potential energy surfaces.

Vibrational properties of C 20 isomers, a semi-empirical study

Self-consisent field Hartree-Fock calculations using MNDO, AM1 and PM3 hamiltonians were carried out for the vibrational spectra of the geometrical isomers of the smallest fullerene cluster, C 20. Comparisons with a recent density functional approach brought out similarities and differences among the methods and were in accord with earlier first principles stability ordering of the three ground state isomers: the planar cyclic form (the ring), the corannulene form (the bowl), and the closed cage fullerene form. Complete vibrational symmetry assignments are given for the fullerene and the bowl forms and an approximate grouping is presented for the ring isomer. The distribution of all vibrational levels is compared among the three forms and the density functional results for the PM3 method, and schematic infrared spectra are calculated for the three C 20 forms.