Vibrational Stark effect: Theoretical determination through the semiempirical AM1 method

The vibrational Stark effect of a series of small molecules has been calculated by means of the semiempirical AM1 method through addition of the electron–field interaction term in the one-electron Hamiltonian. Optimized geometrical parameters along with harmonic frequencies and line intensities are determined for different strengths of the applied uniform electric field. The perturbed spectra are compared with theoretical studies carried out at the ab initio level and with experimental results. The vibrational Stark effect of the retinal molecule is also computed, showing that this kind of study is feasible in systems of biochemical interest. © 1992 by John Wiley & Sons, Inc.     

Green's function method for photoelectron spectroscopy calculations based on MNDO and AM1 semiempirical approximations

Irkutsk State University. Translated from Zhurnal Strukturnoi Khimii, Vol. 30, No. 3, 137–139, May–June, 1989.     

Study of the thermal decomposition of 3-cyclopentenone by using the AM1 semiempirical method

Summary RHF/AM1 and UHF/AM1 low-dimensionality surfaces were calculated by applying the reaction-coordinate technique to the thermal decomposition of 3-cyclopentenone. Several stationary points were accurately located within the entire coordinate space. Although the two formalisms used predicted asynchronous reaction pathways for the process, our results illustrate the limitations of single reference treatments of two-bond reactions while the nature of the reaction path remains uncertain.     

Dimer form of 1,3-dimethyluracil studied by the AM1 semiempirical method

A study of the dimer form of 1,3-dimethyluracil was carried out. The optimum geometric parameters in the monomeric and dimeric forms were obtained using the AM 1 semiempirical method. The results were compared with those reported by X-ray diffraction. The energies in the dimer formation and in the intramolecular C? H···O interaction were calculated. Electronic density maps in two and three dimensions were drawn. Several calculated thermodynamic parameters are discussed. © 1994 John Wiley & Sons, Inc.     

Hydration of small anions: Calculations by the AM1 semiempirical method

The AM1 semiempirical molecular orbital method has been used to calculate successive heats of hydration of small anions, including hydride, hydroxide, and the halogen ions, for cluster sizes up to 11 water molecules surrounding the central anion. Heats of hydration agree with available experimental data to within a few kcal/mol. Structures, however, do not always agree well with available ab initio calculations on clusters with one or two water molecules. The results indicate that the AM1 semiempirical technique applied to finite-sized clusters must be used with caution in understanding how hydration affects the chemical reactions of anions.     

Electronic and structural properties of the metalloporphyrin structural isomers: semiempirical AM1 and PM3 calculations

Semiempirical calculations using AM1 and PM3 have been performed on the zinc(II) and magnesium(II) complexes of nine structural isomers of tetrapyrrole macrocycles such as porphyrin, porphycene, corrphycene and hemiporphycene, N-confused porphyrin and other isomers that have not been synthesized. The optimized geometry and the bond parameters obtained compare favorably with results obtained from X-ray and spectral studies. Heats of formation, ionization potentials, HOMO-LUMO energy differences, dipole moments, and the splitting of HOMOs and LUMOs of the metal complexes of each of these isomers are also reported and compared with experimental results. The “four-orbital model” of Gouterman remains valid for the investigated structural isomers. The present study represents an unusually appropriate opportunity to study, via molecular orbital methods, the interaction between various metal ions, and the electronic and geometrical environment of the central cavity of the closely related isomeric macrocycles. The major outcome of this study is the verification of the expected differential behavior of metal ions employed in the present study as a sophisticated probe of cavity properties which also suggests that this procedure can be extended to other metal complexes. This study also serves as an interesting prototype for more elaborate ab initio calculations. However, such calculations on the presently investigated macrocyclic systems may have to be performed at a higher level than MP2 or DFT to account for the unusual delocalization, as suggested by a recent study by Schaefer and co-workers on delocalized [10]annulene (H.M. Sulzbach, H.F. Schaefer, W. Klopper and H.P. Luthi, J. Am. Chem. Soc., 118 (1996) 3519).     

A study of photoelectron spectra in the framework of the semiempirical AM1 method

The characteristics of photoelectron (PE) spectra of 2-phenylpyrroles and biphenyls have been correlated with the UV spectroscopy data for their radical cations. The geometric and electronic structures of the compounds and radical cations have been calculated using the AM1 method. The absorption bands of the radical cations observed in the visible region of spectrum have been found to pertain to the quasi-Koopmans type,i.e., they are realized between the doubly and partially occupied -MO, but their energies differ strongly from those calculated on the basis of PE spectra. This is explained by the distinction between the spatial structure of a molecule and that of the respective radical cation. The second cause of the discrepancy between the data of the two spectral methods consists in orbital — interactions, which are most conspicuous in the case of 4(4)-halogen-substituted compounds.For Part 4 see ref. 1.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 869–874, May, 1993.     

A study by Raman spectroscopy and the semiempirical AM1 method on several 1,2-dihydroxybenzene solutions

The Raman spectra of 1,2-dihydroxybenzene (catechol) dissolved in six different compounds have been obtained and, on the basis of frequencies and depolarization ratios, the relevant structure of the solute has been inferred in every case. In addition, rotational barrier calculations using the AMI semiempirical method have been performed on several catechol—solvent systems. The theoretical results were in accord with experimental data and were related to structural properties of the solvents.     

Valence-bond calculations on N2 and isoelectronic species

Valence-bond calculations are reported for the isoelectronic series of molecules and ions: N₂, CO, BF, NO⁺ and CN^?. The most important structures are N?N, C?O, B_π? F, N⁺?O and C?N. Hybridization of the 2s and 2p orbitals is important. Only two or three structures are required to obtain an energy lower than that obtained with the molecular orbital approximation. Structures in which the electronegative element loses a σ-orbital or gains a π-orbital are favored. π-bonds tend to be favored over σ-bonds. The bond in NO⁺ resembles that in CO, whereas that in CN^? resembles the bonding in N₂.     

Empirical penetration functions and two-center electron repulsion integrals for semiempirical calculations of electronic structure

Explicit functional forms for both the two-electron Coulomb integral, (aa∣bb), and the one-center core–orbital integrals, Z (aa∣Z_A), are derived which permit the penetration integrals to be fully derived and calculated. With these forms the ³Σ of the H₂ molecule is unstable. These forms are generalized so that they are suitable for optimizing semiempirical predictions of experimental one-electron properties.     

AM1 semiempirical computational analysis of the homopolymerization of spiroorthocarbonate

Spiroorthocarbonates (SOCs) are monomers that have been shown to expand when homopolymerized. SOCs are potential monomer systems that can be combined with other monomers such as epoxy resin to produce a non-shrinking dental matrix for dental composites. The purpose of this study was to use a computer model (AM1) to study possible homopolymerization pathways for several SOC monomers. The gas phase transition states of three feasible reaction mechanisms for the homopolymerization of four spiroorthocarbonate 1,5,7,11-tetraoxaspiro[5,5]undecane (TOSU) systems have been examined using the AM1 semiempirical quantum mechanical model. In addition to the base TOSU noted above, the 2,8-dimethyl, 2,4,8,10-tetramethyl, and the 3,3,9,9-tetramethyl analogs were used in this study. The results of these calculations produced the heats of reaction, activation enthalpies and transition state structures. Our calculations indicate stabilization of the transition states by electron-donating and resonance-stabilizing substituent groups. The energies of activation of all of these systems were between 24 and 38 kcal/mol and all reactions were endothermic. Further, we found that there was a significant intermolecular attraction between TOSU monomers (≈3.5 kcal/mol). When compared with experimental studies of methylated TOSU by Sakai and co-workers, our calculations agree with the preferred site of nucleophilic attack, but not with the experimental rate results. It was concluded that the homopolymerization of the unsubstituted TOSU and its derivatives studied was endothermic and that the rate of homopolymerization of TOSU depends on an intermolecular pre-association of TOSU monomer in the condensed phase.     

Analysis of the core-repulsion functions used in AM1 and PM3 semiempirical calculations: Conformational analysis of ring systems

The AM1 and PM3 potential energy surfaces of cyclopentane have been compared and the energy difference between two (boat and chair) cyclohexane conformers analyzed. The effects of reparameterization and different core-repulsion functions (CRFs) have been studied. The H? H, C? H, and C? C CRF energy contributions have been calculated separately. The results show that the CRF energy corrections stabilize the correct (MM2 and ab initio) geometries. The PM3 equilibrium geometry of cyclopentane is closer to the MM2 and ab initio results than the AM1 geometry. It is known that above 190 pm the AM1 H? H CRF curve is smooth and negative but the PM3 H? H CRF curve has a trough and a shoulder. It has been shown that this latter oscillation is not damped by other parameters. As a result, the H? H PM3 energy gradient curve is different from the quasilinear AM1 and ab initio gradient curves. © 1993 John Wiley & Sons, Inc.     

Interpretation of photoelectron spectra in the AM1 semiempirical method. 3. 2-Substituted benzimidazoles

Analysis of photoelectron spectra of 2-substituted benzimidazoles showed that their orbital structure is determined by the form and energy position of the fragment orbital (-symmetry) of the substituent.For previous communication, see [1].Irkutsk Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, Irkutsk 664033. Translated from Izvestiya Akademii Nauk, Seriya Khimicheskaya, No. 4, pp. 880–884, April, 1992.     

Investigation of UV spectra of isomeric nitropyrazoles by the semiempirical AM1 (CI) method

The absorption bands in the UV spectra of isomeric nitropyrazoles were assigned by the calculations in the semiempirical AMI (CI) approximation. The long-wave absorption of nitropyrazoles is caused by π→π* and η₀→π* transitions. The charge-transfer band is the most intense. The π→π* transitions undergo a considerable bathochromic shift in the deprotonation. The first ionization potential (PI) of the 4-nitropyrazole anion was estimated from the empirical dependence of the energy of the excited π-state on PI of alkyl-substituted 4-nitropyrazoles. The PI of the 4-nitropyrazole anion is 3 eV lower than that of a neutral molecule. This is evidence for a substantial destabilization of the boundary β-orbital in the heterolytic cleavage of the N−H bond. The analysis of the UV and NMR spectra of 3(5)-nitropyrazole confirms the viewpoint that the 3-nitro tautomer predominates in solution. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya. No. 2, pp. 310–314, February, 1997.     

Interpretation of photoelectron spectra within the framework of the AM1 semiempirical method. 2. Pyridines

Analysis of the orbital structure of isomeric pyridines carried out using photoelectron spectroscopy and the AM1 (GF) method showed that this structure is independent of the nature of the substituent at C ²⁽⁶⁾ and C ³⁽⁵⁾ : <n<. All the possible sequences of the highest occupied MO of different symmetry (, ) are realized for 4-substituted pyridines.For previous communication, see [1].Irkutsk Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, Irkutsk 664033. Translated from Izvestiya Akademii Nauk, Seriya Khimicheskaya, No. 4, pp. 872–880, April, 1992.     

Some remarks on the semiempirical one-center electron repulsion integrals

The identification of the stage of ionization for various kinds of one-center electron repulsion integrals, occurring when nonbonding or lone-pair electrons are considered explicitly as well as π-electrons, is discussed for conjugated organic molecules containing heteroatoms N. It is concluded that the value for the negative ions should be used for (π_Cπ_C | π_Cπ_C) in all the states but for (π_Nπ_N | π_Nπ_N) only in the π-π states. In the n-π states, the appropriate value of (π_Nπ_N | π_Nπ_N) is that of the neutral atom if the molecule contains only one N atom. If more than one N atom is involved in the molecule, some weighted mean of the values for the negative ion and for the neutral atom should be used. The value for the neutral atom is most adequate for one-center repulsion integrals other than the (ππ | ππ) type in both the π-π and the n-π states. The method of determining these integrals is also discussed. It is concluded that they are to be determined from the consideration of appropriate electron-transfer reactions except for exchange integrals. The exchange integrals are shown to have to be determined from the Slater–Condon parameters derived from the analysis of the experimental atomic energy levels. Illustrative calculations are given for the lower singlet levels of the formaldehyde, pyrazine, pyridine, and the p-benzoquinone molecule. It is found that the calculated energies of the n-π transitions become much too low unless the (ππ | ππ) values of the heteroatoms in the molecule are chosen differently in the n-π states and in the π-π states as pointed out theoretically in this article.     

Structure-activity relationships of alphaS1-casomorphin using AM1 calculations and molecular dynamics simulations

This paper investigates the structure-activity relationships of alphaS1-casomorphin (alphaS1-CM) using AM1 calculations and molecular dynamics (MD) simulations. Previous studies have shown that this peptide has remarkable opioid actions, and not only has a high affinity toward all three subtypes (kappa1-kappa3) of the kappa-opioid sites, but also inhibits the proliferation of the T47D human breast cancer cell line. The systematic conformer search performed by the AM1 calculations is based on the torsional angles of the Val2-Pro3 (omega2) and Phe4-Pro5 (omega4) amide bonds. The AM1 results reveal that the alphaS1-CM conformers strongly favor the cis/cis pair of the omega2/omega4 amide bonds in the minimized energy state. Furthermore, the picture of these stable conformers is found to be a strong interaction of the coulomb's force between two terminuses. MD simulations are performed to investigate the features of both the structural stability and pharmacological activity of alphaS1-CM in aqueous solution. The simulation results reveal that the omega2/omega4 amide bonds favor the cis/cis status in the stable state. Furthermore, the pharmacophoric distance between two aromatic rings is found to be 5.0 approximately 5.4A. The chi1 rotamers of the Tyr and Phe residues show a preference for gauche (-) and trans, respectively. The side chain rotamers of alphaS1-CM are competed to those of other opioid ligands with a known potency and selectivity for delta- and mu-opioid receptors. Finally, we address a likely kappa pharmacophore model compared to the delta pharmacophore model.