Semiempirical Hamiltonian Research Articles

Molecular Orbital Studies of Crystalline Nitroanilines

The intermolecular interactions leading to crystals of m- and p-nitroaniline have been studied to better understand the interactions that lead to significantly differing crystal structures. Molecular orbital calculations using three semiempirical (AM1, PM3, and SAM1) Hamiltonians are presented for many aggregates containing up to 10 molecules of both m- and p-nitroaniline. The differences in the capacities for hydrogen bonding, both N−H···O and C−H···O, caused by the differing geometries of the monomeric units dictate the different crystal structures. p-Nitroaniline forms H-bonded chains with three-centered H-bonds that allow identical H-bonding on each side to adjacent chains. Thus, they form layers, which then stack (head-to-tail) to form centrosymmetric microcrystals. m-Nitroaniline, on the other hand, forms chains which can form much stronger H-bonds on one side than on the other. Thus, these chains combine in pairs to form “strands” comprised of two chains. These chains then stack in a head-to-head m...

Investigation of hydrogen bond structure in benzoic acid solutions

Significant changes in 13C chemical shifts of benzoic acid (BA) were observed for the carboxyl and quarternary carbon atoms on going from non-polar benzene to solvents with different hydrogen bond donor or acceptor abilities. Shielding effects of 6.145 and 5.413 ppm at the carboxyl carbon in dimethyl sulfoxide (DMSO) and acetone, respectively, are due to the redistribution of electron density upon the formation of new intermolecular hydrogen bonds with solvent molecules. 1H NMR upfield shifts of the carboxyl proton in DMSO and chloroform solutions in comparison with benzene solution, and shifts in the CO stretching frequency, ν CO, observed in infrared spectra of BA complexes are consistent with these results. Structural parameters and interaction energies of the hydrogen-bonded complexes determined by quantum-chemical calculations substantiate the experimental observations. Using the semiempirical PM3 hamiltonian, hydrogen bonding was treated as the donor-acceptor mechanism within the natural bond orbital (NBO) formalism. Two correlations, which reflect hydrogen bonding in different solvents, are proposed: one between the 13C chemical shifts and the change in p-character of the carboxyl carbon atom and the other between the carboxyl CO stretching frequency and the calculated interaction energy of the hydrogen-bonded complexes.

Development of optimized MST/SCRF methods for semiempirical calculations: The MNDO and PM3 Hamiltonians

AbstractThe self‐consistent reaction field (SCRF) method proposed by Miertus, Scrocco, and Tomasi (MST) has been optimized for MNDO and PM3 semiempirical Hamiltonians. Different algorithms used to compute the molecular electrostatic potential (MEP) and different solute cavities have been investigated. The ability of the optimized models to reproduce experimental free energies of solvation and to mimic the solvent effect in several chemical processes has been compared with the ab initio and AM1 versions of the MST method as well as with experimental data. © 1995 by John Wiley & Sons, Inc.

Semi-empirical calculations of intramolecular acyl transfer in cis-enols of O-aroyl acetylacetones

Intramolecular acyl transfer was studied in eight aroyl derivatives of cis enols of acetylacetone using various semiempirical hamiltonians. The transition state geometry and activation energy for each derivative is reported. A reaction rate relative to that for the O-benzoyl derivative was calculated for each member in the series. The calculated relative rate constants were correlated to the substituent electronic constants, σ, and to experimental relative rate constants. Good correlations were obtained in both cases with the exceptions of the p-chloro and m-nitro aroyl groups. The rates of acyl transfer were enhanced by electron withdrawing aroyl groups. Calculations with the PM3 hamiltonians reproduced experimental trends better than using AM1.

Vibrational polarizability of polyacetylene chains

Within the double harmonic oscillator approximation, ab initio vibrational contributions to the static electric dipole polarizability have been computed for the all-trans polyacetylene chains homologous series. Atomic basis set and electron correlation effects have been studied on ethylene and trans-butadiene as well as the use of semiempirical Hamiltonians. By using the 6-31G* atomic basis set within the Hartree–Fock and the second order Mo/ller–Plesset procedures as well as by using semiempirical Austin model 1 Hamiltonians, the evolution with chain length of the vibrational polarizability per structural unit has been investigated and compared to the electronic contribution. Although smaller than the electronic contributions (αvibration≊10% αelectronic), the longitudinal component to the polarizability presents a similar exaltation as chain length grows, but a slower saturation to an asymptotic value per unit cell. Inclusion of electron correlation via the second order Mo/ller–Plesset technique turns out to reduce the longitudinal component calculated at the Hartree–Fock level, but to increase the transversal and perpendicular components. Whereas it reproduces correctly the evolution with chain length of the vibrational polarizability tensor components, the Austin model 1 technique underestimates the longitudinal term and overestimates the perpendicular term. The major contribution to the vibrational polarizability results from large charge fluxes associated with asymmetric stretching motions of the carbon backbone and with the torsion motions presenting very low vibrational frequencies.

Time-dependent theoretical treatments of the dynamics of electrons and nuclei in molecular systems

An overview is presented of methods for time-dependent treatments of molecules as systems of electrons and nuclei. The theoretical details of these methods are reviewed and contrasted in the light of a recently developed time-dependent method called electron-nuclear dynamics. Electron-nuclear dynamics (END) is a formulation of the complete dynamics of electrons and nuclei of a molecular system that eliminates the necessity of constructing potential-energy surfaces. Because of its general formulation, it encompasses many aspects found in other formulations and can serve as a didactic device for clarifying many of the principles and approximations relevant in time-dependent treatments of molecular systems. The END equations are derived from the time-dependent variational principle applied to a chosen family of efficiently parametrized approximate state vectors. A detailed analysis of the END equations is given for the case of a single-determinantal state for the electrons and a classical treatment of the nuclei. The approach leads to a simple formulation of the fully nonlinear time-dependent Hartree-Fock theory including nuclear dynamics. The nonlinear END equations with the [ital ab] [ital initio] Coulomb Hamiltonian have been implemented at this level of theory in a computer program, ENDyne, and have been shown feasible for the study of small molecularmore » systems. Implementation of the Austin Model 1 semiempirical Hamiltonian is discussed as a route to large molecular systems. The linearized END equations at this level of theory are shown to lead to the random-phase approximation for the coupled system of electrons and nuclei. The qualitative features of the general nonlinear solution are analyzed using the results of the linearized equations as a first approximation. Some specific applications of END are presented, and the comparison with experiment and other theoretical approaches is discussed.« less

Aromaticity in metallacyclobutadienes from the perspective of the valence bond theory

The valence bond method has been implemented for the study of π-electron systems using a semiempirical CNDO-type Hamiltonian. The algorithm used is based on the Clifford algebra realization of the Rumer–Weyl basis presented by Paldus et al. Using this version of the CNDO–VB approach, the effect of the metal hybridization in the electronic delocalization of metallacyclobutadienes is discussed. © 1994 John Wiley & Sons, Inc.

MRD‐CI studies of vertical excitation energies of unsaturated hydrocarbon molecules

AbstractSystematic MRD‐CI calculations using the AM1 Hamiltonian have been carried out for two polyenes and eight aromatic hydrocarbons ranging from benzene to ovalene (C32H14). Twenty singlet–singlet excitation energies in these compounds were calculated and compared with experimental data and ab initio STO‐3G results. On an absolute scale, the AM1/MRD‐CI approach underestimates the excitation energies to states with dominant covalent character by an average of 1.1 eV, whereas the errors for ionic states are between −1.0 and 1.0 eV. The STO‐3G calculated data are much too high by ≈ 1 eV and ≈ 5 eV, respectively. The inclusion of σπ‐correlation effects through second‐order Epstein–Nesbet perturbation theory combined with the use of localized orbitals leads to a significant improvement of the ab initio calculated state energies. In an analogous AM1 treatment, negligible corrections for the σπ correlations are found, which is attributed to the implicit account in the parameters and approximation of the semiempirical Hamiltonian. The possible error sources of the calculational methods are discussed. © 1994 by John Wiley & Sons, Inc.

Energy Loss Function for Biological Material: Poly (CSP)

Abstract In this paper calculated cross sections are presented for the interaction of electrons with poly(CSP), a single-stranded chain that contains one cytosine sugar phosphate unit in the elementary cell. To model a single strand of helical DNA (e.g. the base stacking), the Watson-Crick model for the geometry of poly(CSP) has been used. The use, for computational simplicity, of a single, rather than a double stranded polynucleotide may be justified on the basis of previous calculations indicating that - to a good approximation - the electronic structure (other than excitation states) of complementary base pairs may be described as a superposition of the corresponding structures of the individual components. The cross sections are obtained from the dielectric response function of the system, _(q,?), which is calculated with the aid of a semi-empirical Hamiltonian, the parameters of which have been adjusted to fit available optical and electron scattering data on DNA and related systems.

Energy Loss Function for Biological Material: Poly (CSP)

In this paper calculated cross sections are presented for the interaction of electrons with poly(CSP), a single-stranded chain that contains one cytosine sugar phosphate unit in the elementary cell. To model a single strand of helical DNA (e.g. the base stacking), the Watson-Crick model for the geometry of poly(CSP) has been used. The use, for computational simplicity, of a single, rather than a double stranded polynucleotide may be justified on the basis of previous calculations indicating that - to a good approximation - the electronic structure (other than excitation states) of complementary base pairs may be described as a superposition of the corresponding structures of the individual components. The cross sections are obtained from the dielectric response function of the system, _(q,?), which is calculated with the aid of a semi-empirical Hamiltonian, the parameters of which have been adjusted to fit available optical and electron scattering data on DNA and related systems.

The effect of electron donating and electron withdrawing substituents on the degradation rate of bioabsorbable polymers: a semiempirical computational study

The two step hydrolyses of halogen and amine substituted polyglycolic acids are modeled by the semiempirical MNDO hamiltonian using small molecule analogues to determine the effect of the electron donating and withdrawing substituents on the reaction and activation enthalpies. It was seen that halogen substitution on the alkyl portion of the ester increases the rate of hydrolysis by the largest amount, while amino substituents showed much smaller effects. Substitution on the acyl fragment can either accelerate or retard hydrolysis, depending on the relative contributions of the inductive and steric effects.

Electronic structure of U4+, Np4+, and Pu4+ doped into ThSiO4 single crystal

The optical spectra of tetravalent ions of early actinides, U4+, Np4+, and Pu4+, were interpreted via a semiempirical Hamiltonian in D2d site symmetry, in terms of electronic transitions within their respective 5fn ground state configurations. Systematic trends in the semiempirical parameters describing the intraconfiguration transitions have suggested that those for U4+ ion are not representative of the light actinide series.

Molecular dynamics with combined quantum and empirical potentials: C2H2 adsorption on Si(100)

Classical trajectory calculations were employed to study the reaction of acetylene with dimer sites on the Si(100) surface at 105 K. Two types of potential energy functions were combined to describe interactions for different regions of the model surface. A quantum mechanical potential based on the semiempirical AM1 Hamiltonian was used to describe interactions between C2H2 and a portion of the silicon surface, while an empirically parametrized potential was developed to extend the size of the surface and simulate the dynamics of the surrounding silicon atoms. Reactions of acetylene approaching different sites were investigated, directly above a surface dimer, and between atoms from separate dimers. In all cases, the outcome of C2H2 surface collisions was controlled by the amount of translational energy possessed by the incoming molecule. Acetylene molecules with high translational energy reacted with silicon dimers to form surface species with either one or two Si–C bonds. Those molecules with low translational energy either rebounded away from the surface or became trapped in a physisorbed state as evidenced by their bouncing motion above the surface. The reaction of C2H2 to form a bridge between dimers within the same dimer row was found to occur, while bridging between adjacent dimer rows appeared to be unlikely, the C2H2 molecule preferring to migrate to either of the dimers for direct reaction. A mechanism is proposed for chemisorption in which C2H2 first bonds to a dimer site in a mono-σ structure, subsequently attaining the more stable di-σ bonded state through radical–radical recombination. The simulations are consistent with C2H2 adsorption on Si(100) occurring through a mobile precursor mechanism.

Hydrolytic degradation of α‐substituted polyglycolic acids: A semiempirical computational study

AbstractThe two‐step hydrolyses of substituted polyglycolic acids are modeled by the semiempirical MNDO Hamiltonian using small molecule analogs to determine the effect of the alkyl substituents on the reaction and activation enthalpies. Reaction enthalpies remain reasonably constant up to three carbons, before becoming less exothermic for large alkyl substituents. Activation enthalpies show patterns that can be explained by steric effects. © 1993 John Wiley & Sons, Inc.

Theoretical studies applicable to the design of novel anticonvulsants: Part 2. A comparison of AM1, MNDO, and PM3 semiempirical molecular orbital conformational analyses of dihydropyridine calcium channel blockers

The optimization of the anticonvulsant activity of dihydropyridine calcium channel blockers (DHPs) requires suitable structure-activity studies, which in turn require reliable methods of conformational analysis. The utility of AM1, MNDO, and PM3 as methods of conformational analysis for the DHPs was critically assessed. Eighteen DHPs were fully optimized using AM1, MNDO, and PM3, and the results were compared with crystal geometries. AM1 was best suited to the modelling of DHP geometries, based on root mean square fit analysis and the treatment of specific functional groups. The performance of the three techniques was related to the corrective term of the core repulsion function of the semiempirical hamiltonians.

AM1-SM2 and PM3-SM3 parameterized SCF solvation models for free energies in aqueous solution.

Two new continuum solvation models have been presented recently, and in this paper they are explained and reviewed in detail with further examples. Solvation Model 2 (AM1-SM2) is based on the Austin Model 1 and Solvation Model 3 (PM3-SM3) on the Parameterized Model 3 semiempirical Hamiltonian. In addition to the incorporation of phosphorus parameters, both of these new models address specific deficiencies in the original Solvation Model 1 (AM1-SM1), viz., (1) more accurate account is taken of the hydrophobic effect of hydrocarbons, (2) assignment of heavy-atom surface tensions is based on the presence or absence of bonded hydrogen atoms, and (3) the treatment of specific hydration-shell water molecules is more consistent. The new models offer considerably improved performance compared to AM1-SM1 for neutral molecules and essentially equivalent performance for ions. The solute charges within the Parameterized Model 3 Hamiltonian limit the utility of PM3-SM3 for compounds containing nitrogen and possibly phosphorus. For other systems both AM1-SM2 and PM3-SM3 give realistic results, but AM1-SM2 in general outperforms PM3-SM3. Key features of the models are discussed with respect to alternative approaches.

Low-bandgap conjugated polymers. A joint experimental and theoretical study of the structure of polyisothianaphthene

13 C NMR measurements ωere performed on polyisothianaphtene (PITN) and on a series of model isothianaphthene molecules representing either aromatic or quinoid segments of the polymer chain. The chemical shifts of the four carbon of PITN were determined. These values are compared to the data obtained on the model molecules and discussed in terms of the ground state structure (aromatic or quinoid) of the polymer. Quantum-chemical calculations using the Austin model 1 semiempirical Hamiltonian are performed on ITN oligomers of various lengths. The relative stabilities of the aromatic and quinoid valence bond isomers are estimated in relation to the corresponding values for polythiophene

PM3‐SM3: A general parameterization for including aqueous solvation effects in the PM3 molecular orbital model

AbstractOur recently proposed scheme for including aqueous solvation free energies in parameterized NDDO SCF models is extended to the Parameterized Model 3 semiempirical Hamiltonian. The solvation model takes accurate account of the hydrophobic effect for hydrocarbons, as well as electric polarization of the solvent, the free energy of cavitation, and dispersion interactions. Eight heteroatoms are included (along with H and C), and the new model is parameterized accurately for the water molecule itself, which allows meaningful treatments of specifically hydrogen bonded water molecules. The unphysical partial charges on nitrogen atoms predicted by the Parameterized Model 3 Hamiltonian limit the accuracy of the predicted solvation energies for some compounds containing nitrogen, but the model may be very useful for other systems, especially those for which PM3 is preferred over AM1 for the solute properties of the particular system under study. © 1992 by John Wiley & Sons, Inc.

Semiempirical calculations of hyperpolarizabilities for extended π systems: Polyenes, polyynes, and polyphenyls

AbstractThe dipole moments (μ), polarizabilities (α), hyperpolarizabilities (β), and second‐order hyperpolarizabilities (γ) of polyenes, polyynes, and polyphenyls have been calculated by a finitefield method with the PM‐3 parameterization of the semiempirical MNDO Hamiltonian at the optimum geometries. These results were compared to experimental values obtained from EFISH and THG measurements. The calculations reproduce the magnitudes of β and γ, as well as the effect of the substituents and the effect of bond alternation on β and γ. The coefficients of the power law, which describes the dependence of β and γ on the number of π centers, were calculated. For β, exponents of 1.5–2.2 and 0.03–0.04 were obtained for polyenes and polyynes, respectively, and for γ, exponents of 3.9–4.9, 2.9–3.3, and 2.5–2.7 were obtained for polyenes, polyynes, and polyphenyls, respectively. These results confirm the efficiency of enhancing γ by insertion of C = C double bonds into a chain. © 1992 John Wiley & Sons, Inc.

Theoretical studies on the core structure of the 450 degreesC oxygen thermal donors in silicon.

Results of molecular- and cyclic-cluster calculations using semiempirical Hamiltonians on a wide range of small oxygen complexes in crystalline silicon are reported. It is shown that a core involving (at most) two oxygens and a self-interstitial can explain the observed behavior of the thermal-double-donor complexes arising in silicon after heat treatment around 450 \ifmmode^\circ\else\textdegree\fi{}C, while all other oxygen complexes proposed so far can be excluded as the core of these centers.