Quantum-chemical study of photoisomerization and photoinduced proton transfer in hydroxystyrylquinolines

The structures of 2-(4-hydroxystyryl)quinoline 1 and 2-(2-hydroxystyryl)quinoline 2 have been optimized by the semiempirical methods PM3 and PM3-CI(8 × 8) with configuration interaction for the ground (S₀) and the excited singlet (S₁) states, respectively. The relative stability of the E- and Z-isomers, the quinoid tautomers, and the spiropyran form for compound 2 was calculated. It was found that hydroxyl-containing tautomers were more stable in the S₀ state, and the quinoid tautomers are more stable in the S₁ state. The calculations predict the possibility of photoisomerization and photoinduced proton transfer in hydroxystyrylquinolines.     

Pyrrolizidine alkaloids necine bases: Ab initio,semiempirical, and molecular mechanics approaches to molecular properties

The structural stabilities of endo and exo conformations of retronecine and heliotridine molecules were analyzed using different ab initio, semiempirical, and molecular mechanics methods. All electron and pseudopotential ab initio calculations at the Hartree-Fock level of theory with 6-31G* and CEP-31G* basis sets provided structures in excellent agreement with available experimental results obtained from X-ray crystal structure and ¹H-NMR (nuclear magnetic resonance) studies in D₂O solutions. The exo conformations showed a greater stability for both molecules. The most significant difference between the calculations was found in the ring planarity of heliotridine, whose distortion was associated with the interaction between the O(11)H group and the C(1)-C(2) double bond as well as with a hydrogen bond between O(11)H and N(4). The discrepancy between pseudopotential and all-electron optimized geometries was reduced after inclusion of the innermost electrons of C(1), C(2), and N(4) in the core potential calculation. The MNDO, AM1, and PM3 semiempirical results showed poor agreement with experimental data. The five-membered rings were observed to be planar for AM1 and MNDO calculations. The PM3 calculations for exo-retronecine showed a greater stability than the endo conformer, in agreement with ab initio results. A good agreement was observed between MM3 and ab initio geometries, with small differences probably due to hydrogen bonds. While exo-retronecine was calculated to be more stable than the endo conformer, the MM3 calculations suggested that endo-heliotridine was slightly more stable than the exo form. © 1996 by John Wiley & Sons, Inc.     

On the conformation of the propranolol molecule

The structure of the propranolol molecule has been optimized within the AM1 and PM3 semiempirical framework followed by ab initio HF/6-31G^* refinement. On each calculation level the conformational space was sampled to search for the lowest-energy conformer(s) from among a few hundreds of conformers at the semiempirical step and next from among a few dozens of conformers at the ab initio level. Finally, five stable conformers were found; each stabilized by one or two of the three possible hydrogen bonds. The geometrical and electronic parameters were established and found to differ only slightly in the structures with the hydrogen bond either present or not.     

Study of hydrogen bonding interactions relevant to biomolecular structure and function

Ab initio molecular orbital calculations were used to study hydrogen bonding interactions and interatomic distances of a number of hydrogen bonded complexes that are germane to biomolecular structure and function. The calculations were carried out at the STO-3G, 3-21G, 6-31G*, and MP2/6-31G* levels (geometries were fully optimized at each level). For anionic species, 6-31 + G* and MP2/6-31 + G* were also used. In some cases, more sophisticated calculations were also carried out. Whenever possible, the corresponding enthalpy, entropy, and free energy of complexation were calculated. The agreement with the limited quantity of experimental data is good. For comparison, we also carried out semiempirical molecular orbital calculations. In general, AM1 and PM3 give lower interaction enthalpies than the best ab initio results. With regard to structural results, AM1 tends to favor bifurcated structures for O? H-O and N? HO types of hydrogen bonds, but not for hydrogen bonds involving O-H? S and S-H? O, where the usual hydrogen bond patterns are observed. Overall, AM1 geometries are in general in poor agreement with ab initio structural results. On the other hand, PM3 gives geometries similar to the ab initio ones. Hence, from the structural point of view PM3 does show some improvement over AM1. Finally, insights into the formation of cyclic or open formate–water hydrogen bonded complexes are presented. © 1992 by John Wiley & Sons, Inc.     

Electronic and steric effect manifestations in the structure of 9-Azidoacridine

The crystal structure of 9-azidoacridine (9AA) was determined by X-ray structure analysis (the compound crystallizes in the rhombic system). The crystallographically independent fragment of the structure of 9AA was found to contain two molecules. Both molecules were nonplanar, and the azido group was displaced out of the acridine nucleus plane by 34.6° (molecule A) and 28.6° (molecule B). The barriers to azido group rotations about the C-N bond were calculated by the semiempirical PM3 and nonempirical DFT B3LYP quantum-chemical methods. According to the B3LYP/6-31G^* calculations, the structures with the azido group situated in the acridine nucleus plane and perpendicularly to this plane are 0.21 and 1.66 kcal/mol, respectively, higher in energy than the completely optimized structure, in which the dihedral angle between the azido group and acridine nucleus planes is 32°. The PM3 method overestimates the steric strain energy of 9AA and underestimates the energy of azido group conjugation with the acridine nucleus compared with B3LYP calculations.     

Improving description of hydrogen bonds at the semiempirical level: water–water interactions as test case

Hydrogen bonding is not well described by available semiempirical theories. This is an important restriction because hydrogen bonds represent a key feature in many chemical and biochemical processes, besides being responsible for the singular properties of water. In this study, we describe a possible solution to this problem. The basic idea is to replace the nonphysical gaussian correction functions (GCF) appearing in the core–core repulsion terms of most MNDO‐based semiempirical methods by a simple function exhibiting the correct physical behavior in the whole range of intermolecular separation distances. The parameterized interaction function (PIF) is the sum of atom‐pair contributions, each one having five adjustable parameters. In this work, the approach is used to study water–water interactions. The parameters are optimized to reproduce a reference ab initio intermolecular energy surface for the water–water dimer obtained at the MP2/aug‐cc‐pVQZ level. OO, OH, and HH parameters are reported for the PM3 method. The results of PM3‐PIF calculations remarkably improve qualitatively and quantitatively those obtained at the standard PM3 level, both for water–dimer properties and for water clusters up to the hexamer. For example, the root‐mean‐square deviation of the PM3‐PIF interaction energies, with respect to ab initio values obtained using 700 points of the water dimer surface, is only 0.47 kcal/mol. This value is much smaller than that obtained using the standard PM3 method (4.2 kcal/mol). The PM3‐PIF water dimer energy minimum (−5.0 kcal/mol) is also much closer to ab initio data (−5.0±0.01 kcal/mol) than PM3 (−3.50 kcal/mol). The method is therefore promising for the development of new semiempirical approaches as well as for application of combined quantum mechanics and molecular mechanics techniques to investigate chemical processes in water. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 572–581, 2000     

Semiempirical and DFT computations of the influence of Tb(III) dopant on unit cell dimensions of cerium(III) fluoride

Several computational methods, both semiempirical and ab initio, were used to study the influence of the amount of dopant on crystal cell dimensions of CeF₃ doped with Tb³⁺ ions (CeF₃:Tb³⁺). AM1, RM1, PM3, PM6, and PM7 semiempirical parameterization models were used, while the Sparkle model was used to represent the lanthanide cations in all cases. Ab initio calculations were performed by means of GGA+U/PBE projector augmented wave density functional theory. The computational results agree well with the experimental data. According to both computation and experiment, the crystal cell parameters undergo a linear decrease with increasing amount of the dopant. The computations performed using Sparkle/PM3 and DFT methods resulted in the best agreement with the experiment with the average deviation of about 1% in both cases. Typical Sparkle/PM3 computation on a 2×2×2 supercell of CeF3:Tb3+ lasted about two orders of magnitude shorter than the DFT computation concerning a unit cell of this material. © 2014 Wiley Periodicals, Inc.     

PM3 semiempirical study and its comparison with X-ray crystal structure of 2-methyl-4-(4-methoxyphenylazo)phenol

The crystal and molecular structure of 2-methyl-4-(4-methoxyphenylazo)phenol have been determined by X-ray single crystal diffraction technique. The compound crystallizes in the monoclinic space group P2₁/c with a=9.7763(8) Å, b=11.3966(8) Å, c=11.9531(8) Å and β=108.752(6)°. In addition to the molecular geometry from X-ray experiment, its optimized molecular structure has been obtained with the aid of PM3 semiempirical quantum mechanical method, and then the corresponding geometric parameters were compared with those of X-ray crystallography. To determine conformational flexibility and crystal packing effects on the molecules, molecular energy profile of the title compound was obtained with respect to two selected degrees of torsional freedom, which were varied from ?180° to +180° in steps of 10°. Crystal structure of the title compound is a fibroid structure constructed by C–H···O and O–H···N type intermolecular hydrogen bonds. The most favorable conformer of the title compound has been determined by the crystal packing effects and there is no steric hindrance during rotation around the selected torsion angles.     

Molecular structure and electronic spectrum of ellagic acid: Semiempirical molecular orbital calculations

The molecular structure of ellagic acid has been optimized by using PM3 semiempirical MO method. Ellagic acid has been calculated to be planar with the molecular symmetry of C_2h. The lactone carbonyl groups are not tilted from the molecular plane. CNDO/S MO method has been used to interpret the experimental uv-vis spectroscopic data. The results of the PM3 and CNDO/S calculations have been in good agreement with the experimental data.     

Can semi-empirical models describe HCl dissociation in water?

We discuss the failure of commonly used AM1 and PM3 semiempirical methods to correctly describe acid dissociation. We focus our analysis on HCl because of its physicochemical importance and its relevance in atmospheric chemistry. The structure of non-dissociated and dissociated HCl – (H₂O) _n clusters is accounted for. The very bad results obtained with PM3 (and also with AM1) are related to large errors in gas-phase proton affinity of water and gas-phase acidity of HCl. Indeed, estimation of pKa values shows that neither AM1 nor PM3 are able to predict HCl dissociation in liquid water since HCl is found to be a weaker acid than H₃O⁺. We have proposed in previous works a modified PM3 approach (PM3-MAIS) adapted to intermolecular calculations. It is derived from PM3 by reparameterization of the core–core functions using ab initio data. Since parameters for H–Cl and O–Cl core–core interactions were not yet available, we have carried out the corresponding optimization. Application of the PM3-MAIS method to HCl dissociation in HCl–(H₂O) _n clusters leads to a huge improvement over PM3 results. Though the method predicts a slightly overestimated HCl acidity in water environment, the overall agreement with ab initio calculations is very satisfying and justifies efforts to develop new semiempirical methods.     

Correlation of singlet-triplet gaps for aryl carbenes calculated by MINDO/3, MNDO,AM1, and PM3 with Hammett-type substituent constants

Heats of formation, atomic charges, and geometries of some 110 structures involving substituted singlet and triplet phenyl and 4,4-dimethyl-1,4-dihydronaphthalene carbenes and the corresponding diazomethanes were calculated by MINDO/3, MNDO, AM1, and PM3 semiempirical molecular orbital methods. The singlet-triplet gaps for AM1 and PM3 calculations for the para derivatives in both systems have been successfully correlated with Brown σ⁺ constants. Good correlations with σ⁺ were found for the charges on the carbenic centers of the singlets as well as with the energy barrier for rotation of the aryl group about the C-C single bond in substituted singlet phenylcarbenes. Comparisons of these results with experimental data indicate that AM1 and PM3 are much better than MNDO and MINDO/3 in predicting the intrinsic substituent effects in singlet carbenes.     

A computational study of the reaction of methane with methyl radical

The activation energy and optimized transition-state geometry for the abstraction of a hydrogen atom from methane by methyl radical have been calculated by the semiempirical methods MINDO /3 and MNDO . These results are compared with other semiempirical and ab initio results. The MINDO /3 method, based upon accuracy of the computed energy of activation, appears to be the computational method of greatest reliability. A method of locating the transition state on semiempirical surfaces is demonstrated.     

Generalized hybrid orbital for the treatment of boundary atoms in combined quantum mechanical and molecular mechanical calculations using the semiempirical parameterized model 3 method

The application of combined quantum mechanical (QM) and molecular mechanical methods to large molecular systems requires an adequate treatment of the boundary between the two approaches. In this article, we extend the generalized hybrid orbital (GHO) method to the semiempirical parameterized model 3 (PM3) Hamiltonian combined with the CHARMM force field. The GHO method makes use of four hybrid orbitals, one of which is included in the QM region in self-consistent field optimization and three are treated as auxiliary orbitals that do not participate in the QM optimization, but they provide an effective electric field for interactions. An important feature of the GHO method is that the semiempirical parameters for the boundary atom are transferable, and these parameters have been developed for a carbon boundary atom consistent with the PM3 model. The combined GHO-PM3/CHARMM model has been tested on molecular geometry and proton affinity for a series of organic compounds.Acknowledgement We thank the National Institutes of Health for support of this research.Contribution to the Jacopo Tomasi Honorary Issue     

Design of a Three Component Crystal Based on the Cocrystal of Phenazine and 2,2′-Dihydroxybiphenyl

The preparation of a three component crystal of 2,2-dihydroxybiphenyl (1), phenazine (2) and acridine (3) is described whose possible existence was produced from the structure of a 2:3 cocrystal of 2,2-dihydroxybiphenyl (1) and phenazine (2). X-Ray structures of both crystals are reported. Inspection of the crystal lattice of the 2:3 cocrystal shows that one phenazine molecule forms one and the other two hydrogen bonds to hydroxygroups of the diol. The molecule forming only one hydrogen bond can be replaced successfully by acridine, a one-hydrogen bond acceptor.     

Computational structural determination and energy landscape analysis of the hepatic carcinogen 2-(acetylamino)fluorene

 2-(Acetylamino)fluorene (AAF), a potent mutagen and a prototypical example of the mutagenic aromatic amines, forms covalent adducts to DNA after metabolic activation in the liver. A benchmark study of AAF is presented using a number of the most widely used molecular mechanics and semiempirical computational methods and models. The results are compared to higher-level quantum calculations and to experimentally obtained crystal structures. Hydrogen bonding between AAF molecules in the crystal phase complicates the direct comparison of gas-phase theoretical calculations with experiment, so Hartree–Fock (HF) and Becke–Perdew (BP) density functional theory (DFT) calculations are used as benchmarks for the semiempirical and molecular mechanics results. Systematic conformer searches and dihedral energy landscapes were carried out for AAF using the SYBYL and MMFF94 molecular mechanics force fields; the AM1, PM3 and MNDO semiempirical quantum mechanics methods; HF using the 3-21G*and 6-31G* basis sets; and DFT using the nonlocal BP functional and double numerical polarization basis sets. MMFF94, AM1, HF and DFT calculations all predict the same planar structures, whereas SYBYL, MNDO and PM3 all predict various nonplanar geometries. The AM1 energy landscape is in substantial agreement with HF and DFT predictions; MMFF94 is qualitatively similar to HF and DFT; and the MNDO, PM3 and SYBYL results are qualitatively different from the HF and DFT results and from each other. These results are attributed to deficiencies in MNDO, PM3 and SYBYL. The MNDO, PM3 and SYBYL models may be unreliable for compounds in which an amide group is immediately adjacent to an aromatic ring. Received: 26 May 2002 / Accepted: 12 December 2002 / Published online: 14 February 2003     

Design,synthesis and application of new bile acid ligands with 1,2,3-triazole ring

New dimers have been obtained from propargyl ester of bile acids and α,α′-diazide-m-xylene by intermolecular 1,3-dipolar cycloaddition. These compounds have been used as ligands to form intermolecular hydrogen bonds with various aromatic acids. The structures of all products were confirmed by spectroscopic (¹H NMR, ¹³C NMR and FT-IR) analysis, mass spectrometry (ESI, MALDI) and PM5 semiempirical methods.     

Activation Energy and Transition State Determination of the Olefin Insertion Process of Metallocene Catalysts Using a Semiempirical Molecular Orbital Calculation

The transition state of the olefin insertion process of metallocene catalysts can be determined by adopting the semiempirical PM3 model. In computational chemistry, the computational methods most employed are the ab initio method and density functional theory, which are very time consuming. The semiempirical molecular orbital method requires much less computational resources than the above methods. However, the accuracy and reliability of the semiempirical molecular orbital method remains to be determined. The PM3 model is the most recently developed the semiempirical molecular orbital method and can also be applied to transition metal calculations. This study is intended to investigate the reliability of computational results determined using semiempirical PM3 model on metallocene catalysts through comparison with published results on the density functional theory (DFT). The saddle point finding procedure is adopted to find the transition state of the ethylene insertion process of metallocene catalysts. Results on the geometry and energy trends of the ethylene insertion process of metallocene catalysts determined using the PM3 model are in good agreement with the DFT results. In addition, the saddle point of the potential energy surface of ethylene insertion is verified in accordance with the eigenvalue of the vibrational frequency spectrum. Correct eigenvalues indicate that the correct saddle point of the potential energy surface of ethylene insertion has been successfully located. Hence, the eigenvalue of the vibrational frequency spectrum is a valuable reference in terms of saddle point justification. Computational results and vibrational frequency spectrum analysis demonstrate that the PM3 model can be used to locate the correct saddle point of the potential energy surface. The results obtained using the PM3 model confirm that the eigenvalue of the transition state lies nearly on the vibrational frequency spectrum. The eigenvalues are also analyzed, providing a valuable reference for further studies of the transition state of olefin insertion of metallocene catalysts. The activation energies for the olefin insertion reaction are also studied for evaluation of the catalyst.     

Complexes of lasalocid 2-naphthylmethyl ester with monovalent metal cations studied by mass spectrometry, spectroscopic and semiempirical methods

Lasalocid acid is an ionophore able to carry protons and cations through the cell membrane. Its 2-naphthylmethyl ester (NAFB) and its complexes with Li⁺, Na⁺ and K⁺ cations were synthesized and their structures were studied by ESI-MS, ¹H NMR, ¹³C NMR, FTIR and PM5 methods. The ESI-MS spectra indicate that NAFB forms stable complexes with Li⁺, Na⁺ and K⁺ cations of exclusively 1:1 stoichiometry and that the complexation of Li⁺ cations by NAFB is favoured. The NMR and FTIR spectra indicate that the oxygen atom of the ketone group of the NAFB molecule is involved in the coordination of the cations, and the strength of this process is dependent on the type of cation. We find that the intramolecular O(3)?CH···O(2) hydrogen bond in NAFB and its complexes is partially broken in acetonitrile solution and that this process is independent of the type of cation. The PM5 semiempirical calculations allow visualisation of all structures and determination of the hydrogen bond parameters.     

Pericyclic and Heteroelectrocyclic Mechanisms for the Cyclization of 1,3,5-Hexatrien-1-one and Its 6-Aza Analog

The cyclization of 1,3,5-hexatrien-1-one, 1, and the Z- and E-isomers of 1-aza-1,3-butadienylketene 3 were studied using the semiempirical AM1 and PM3 methods. Cyclizations of compounds 1 and Z-3 are shown to occur via a mono-rotation mechanism with barriers of 15.49 and 32.85 kcal/mol respectively. The reactions proceed via non-planar transition states which result from rotation of the methylene group for compound 1 and the imino group for compound Z-3. Cyclization of E-3 proceeds via a non-rotatory mechanism through a planar transition state. The activation barrier is 4.83 kcal/mol (AM1). The electronic structures of the initial and final states, and of some intermediate structures, including the transition states for the cyclization of compounds 1 and 3, were analyzed by the natural orbital method using HF/6-31G*//AM1 calculations. Energetic, structural, and orbital criteria indicate the heteroelectric mechanism for the cyclization of compound E-3 and the pericyclic mechanism for the cyclization of compounds 1 and Z-3.     

Electronic structures and properties of the rhenium alkoxo derivatives Re2O3(OMe)6, Re4O6(OMe)12, and ReMoO2(OMe)7

The geometrical structures, charge distributions, dipole moments, frequencies of normal vibrations, NMR spectra, and total energies of the chemical bonds for the rhenium alkoxo derivatives Re₂O₃(OMe)₆, Re₄O₆(OMe)₁₂, and ReMoO₂(OMe)₇ were calculated by the DFT-B3LYP and Hartree-Fock ab initio methods based on the effective core potential theory (LANL2DZ approximation) and the semiempirical PM3(tm) method. Two optimized structures of Re₂O₃(OMe)₆ with close energies were found to substantially differ in geometry, ¹H, ¹³C, and 1¹⁷O NMR spectra, and dipole moment. Various characteristics of the electronic structures and the trans-effect of the ligands in the compounds under consideration were discussed.