AM1 Hamiltonian Research Articles

Structures, stabilities and isomerism in C 60H 36 and C 60F 36. A comparison of the AM1 Hamiltonian and density functional techniques

The study of the structures and stabilities of the more stable isomers of C 60H 36 and C 60F 36, previously found in broad surveys using the AM1 Hamiltonian and the program mopac 6.0, has been extended with the density functional technique B3LYP/6-31G ∗ using gaussian 98. The density functional calculations favour structures with unhydrogenated and unfluorinated C 6 rings whereas the AM1 calculations favour structures with isolated carbon–carbon double bonds. The density functional calculations reveal a remarkable diversity in the types of structure for the more stable isomers. The most stable isomer for both C 60H 36 and C 60F 36 has four bare C 6 rings as far apart as possible. The second most stable isomer has three bare C 6 rings with three isolated CC units on pent–hex edges. The next three isomers have two bare C 6 rings which may be as far apart as possible or both be on the same side of the molecule, while the CC bonds on pent–hex edges may be isolated from each other or form C 4 units.

QSPR Analysis of Phenylthio Phenylsulfinyl and Phenylsulfonyl Esters Using Quantum Chemical Semi‐Empirical Descriptors

AbstractQuantitative structure‐property relation ships (QSPR) were developed with the quantum semiempirical descriptors computed by AM1 Hamiltonian in MOPAC7.0 for phenylthio, phenylsulfinyl and phenylsulfonyl esters. Using step wise regression analysis with a cross‐validation procedure, the most potent and in formative descriptors were screened out from a group of 19 quantum chemical semi‐empirical descriptors, including steric and electronic types, to build QSPR models. Several equations were obtained and used to estimate and predict octanol/water partition coefficients and reversed phase high‐performance liquid chromatography (HPLC) capacity factors for a series of 30 similar sulfur‐containing compounds. The results indicate that molecular descriptors, including average molecular polarizability (α), energy of the lowest unoccupied molecular orbital (ELUMO), net atomic charge on carbon atoms in the carbonyl (QCO), molecular weight (MW), the most positive atomic charge on hydrogen atom (QH+), and net atomic charge on oxygen atoms in the group‐NO2 (QNQ2) are the main factors affecting the octanol/water partition coefficients of the compounds under study. And quantum descriptors, covering the most negative atomic charge on an atom Q−), net atomic charge on carbon atoms in the carboxy (QCOO), molecular weight (MW), heat of formation (HF), the most positive atomic charge on a hydrogen atom (QH+), and total energy (TE), are the main factors affecting HPLC capacity factors of these compounds. Rational mechanisms for the two physico‐chemical proper ties of the sulfur‐containing carboxylates were discussed and interpreted.

Synthesis and nicotinic binding studies on enantiopure diazine analogues of the novel (2-chloro-5-pyridyl)-9-azabicyclo[4.2.1]non-2-ene UB-165.

As part of our program aimed at optimizing therapeutic effects over toxic effects (as observed in the naturally occurring nicotinic acetylcholine receptor modulators (-)-nicotine, (-)-epibatidine, (-)-ferruginine, and (+)-anatoxin-a), we investigated the bioisosteric potential of diazines in the field of (+)-anatoxin-a-type structures. In the series of diazine analogues of deschloro-UB-165 (DUB-165, 6), bioisosteric replacement of the 3-pyridyl pharmacophoric element by a 4-pyridazinyl, 5-pyrimidinyl, or 2-pyrazinyl moiety resulted in novel nAChR ligands 7, 8, and 9. A palladium-catalyzed Suzuki cross-coupling of the 3-diethylboranylpyridine (14) and a Stille cross-coupling of the corresponding tributylstannyl diazines 15-17 with the vinyl triflate 13 of the N-protected 9-azabicyclo[4.2.1]nonan-2-one 12 constitute the key steps in the syntheses of these enantiopure anatoxinoids 6-9. Studies of the in vitro affinity for (alpha4)(2)(beta2)(3), alpha3(beta)4, and alpha7 nAChR subtypes by radioligand binding assays demonstrated that the diazine analogues 7-9 can be considered as pharmacologically attractive bioisosteres of DUB-165 (6) but with different effects on the binding affinity with regard to the diazine moiety. The pyrimidine-containing bioisostere 8 turned out to be the most active diazine analogue, which interacts potently (K(i) = 0.14 nM) with the (alpha4)(2)(beta2)(3) subtype and differentiates significantly among the nAChR subtypes investigated. The nitrogens in this anatoxinoid 8 show by far the most negative atomic charges (calculated using the AM1 Hamiltonian). This qualitatively correlates with the highest binding affinity observed for 8 for all subtypes under consideration.

Structures of C70X42 and C70X44, X=H, F

The structures and stabilities of C70X42 and C70X44 where X is H or F, have been investigated using the AM1 Hamiltonian and the program mopac 6.0. As in C70X36, C70X38 and C70X40, structures are based on an equatorial plane of ten bare carbon atoms separating two C30 hemispheres which do not interact strongly with each other. In C70X42 there is a C30X20 hemisphere and a C30X22 hemisphere whereas in C70X44 there are two C30X22 hemispheres. Within each hemisphere, the bare carbon atoms are grouped as isolated C6 rings or as isolated CC units. The C30X20 hemisphere was the same as in C70X38 and C70X40. All 126 possible C30X22 hemispheres were considered. Each of these hemispheres has five rotation positions relative to the other hemisphere, and the 106, which do not have a mirror plane exist as a pair of optical enantiomers. The most stable isomers for C70F42 and C70F44 contain two unfluorinated C6 rings as was also found for C70F40. In contrast to C70F38, C70F40 and C70F42, there is one isomer of C70F44 which may be significantly more stable than all other isomers. The most stable isomers of C70H42 and C70H44 are different to the fluorides and there are many isomers of the hydrides of comparable stability with zero, one or two unhydrogenated C6 rings.

Electronic structure of poly(iminomethylene) using semi-empirical methods

The electronic structure of poly(iminomethylene), the parent polymer for a class of rigid rod polymers known as polyisocyanides, has been studied by semi-empirical methods using the AM1 and PM3 hamiltonians. All of the possible helical geometries, 2 1, 3 1 and 4 1, as well as pseudo-helical and more generalized geometries have been studied. The most stable geometry is a generalized structure with four residues per translational unit, which is only slightly distorted from a helical geometry. It is an isotactic geometry, with the hydrogen substituents directed parallel to the screw direction. The most stable helical geometry has three residues per translational unit. The C–C bond lengths for the 2 1 geometries are longer than those for the 3 1 and 4 1 geometries, but the calculated band gaps are smaller for the former. The calculated density of states for the 3 1 and 4 1 geometries are not highly correlated. For a set of polyisocyanides with the same conformation, the density of states of the parent polymer is expected to be a good approximation to the backbone density of states of the members of the set.

Predicting partitioning of volatile organic compounds from air into plant cuticular matrix by quantum chemical de-scriptors

Based on theoretical linear solvation energy relationship and quantum chemical descriptors computed by AM1 Hamiltonian, a new model is developed to predict the partitioning of some volatile organic compounds between the plant cuticular matrix and air.

The effect of precision of molecular orbital descriptors on toxicity modeling of selected pyridines

The response-surface approach to QSARs attempts to model toxic potency of diverse groups of chemicals while avoiding problems associated with the identification of the mechanism of toxic action or specific chemical class often associated with other approaches. However, while hydrophobicity-dependent, simple regression QSARs derived for congeneric series of organic compounds typically have coefficients of determination greater than 0.90, more heterogeneous multiple regression QSARs exhibit typically 10-15% more unexplained variability. One difference between these approaches is the use of a quantum chemical (QC) descriptor, particularly molecular orbital (MO) energy values such as the energy of the lowest unoccupied molecular orbital ( E LUMO ). The reduced statistical fit exhibited by QSAR models, which include these QC-MO descriptors, could be a result of the variability inherent in the calculation of these descriptors. The present investigation with a structurally and mechanistically diverse set of pyridines revealed that variability is associated with the calculation of the MO descriptor E LUMO both between selected Hamiltonians and selected software packages. However, this variability in no way affects the statistical significance of QSARs for toxicity using these values. Specifically, the E LUMO values calculated with the PM3 and AM1 Hamiltonians in the two software packages were highly related. There was no relationship between molecular complexity or chemical reactivity and increased differences in individual E LUMO values as described by the standard errors of the mean. Although nine appeared to be the number of calculations, which best minimizes the standard error in energy values relative to computational costs; this minimization did not alter the statistics of the QSARs derived with single vs. mean E LUMO values. While the energy of the highest occupied molecular orbital ( E HOMO ) values were not used in the modeling of toxicity, a comparison of these values revealed greater variability between the Hamiltonians and software packages than observed for E LUMO values. Examination of the magnitudes of standard error of the E HOMO values in connection to structural features or reactivity likewise revealed no trends.

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.

Molecular structures of carotenoids as predicted by MNDO-AM1 molecular orbital calculations

Semi-empirical molecular orbital calculations using AM1 Hamiltonian (MNDO-AM1 method) were performed for a number of biologically important carotenoid molecules, namely all- trans-β-carotene, all- trans-zeaxanthin, and all- trans-violaxanthin (found in higher plants and algae) together with all- trans-canthaxanthin, all- trans-astaxanthin, and all- trans-tunaxanthin in order to predict their stable structures. The molecular structures of all- trans-β-carotene, all- trans-canthaxanthin, and all- trans-astaxanthin predicted based on molecular orbital calculations were compared with those determined by X-ray crystallography. Predicted bond lengths, bond angles, and dihedral angles showed an excellent agreement with those determined experimentally, a fact that validated the present theoretical calculations. Comparison of the bond lengths, bond angles and dihedral angles of the most stable conformer among all the carotenoid molecules showed that the displacements are localized around the substituent groups and hence around the cyclohexene rings. The most stable conformers of all- trans-zeaxanthin and all- trans-violaxanthin gave rise to a torsion angle around the C6–C7 bond to be ±48.7 and −84.8°, respectively. This difference is a key factor in relation to the biological function of these two carotenoids in plants and algae (the xanthophyll cycle). Further analyses by calculating the atomic charges and using enpartment calculations (division of bond energies between component atoms) were performed to ascribe the cause of the different observed torsion angles.

ELECTRO-ABSORPTION SPECTROSCOPY AND SEMI-EMPIRICAL MOLECULAR ORBITAL CALCULATIONS OF POLAR RETINOID ANALOGUES

Nonlinear polarizabilities of a series of polar retinoid analogues were determined experimentally by means of electro-absorption (Stark) spectroscopy. The dependence of the magnitude of nonlinear polarizabilities on polyene chain-lengths as well as on the strength of electron-accepting groups was systematically compared. Semi-empirical molecular orbital calculations using AM1 Hamiltonian (MNDO-AM1 method) could quantitatively predict the second (β) and the third (γ) order nonlinear polarizabilities of the present set of molecules except for the γ value of C20BDCInd. The real and imaginary parts of χ(3)(-ω;0,0,ω) spectra were calculated in order to account the figure of merit of the third-order nonlinear optical material.

Hatch opening and closing on oxygenation and deoxygenation of C 60 bathysphere

The structures and stabilities of C 60O n , where n=1–6, 9, have been calculated using the AM1 Hamiltonian and the program mopac 6.0, and by the density functional technique B3LYP/6-31G* at the AM1 geometry using Gaussian 98. Modes of oxygen addition considered were ethers, epoxides, ketones and ketenes. It is confirmed that in C 60O a carbon–carbon bond on a pent–hex edge is replaced by an ether linkage. For higher levels of oxygen addition the replacement of a carbon–carbon bond by two ketone groups becomes important. Particularly stable structures are formed if the additions are on the same, or adjacent, C 6 rings of the C 60 structure where the oxygen atoms cooperate in opening up large holes in the molecule. Molecules of greatest stability have a mixture of ether oxygen atoms on pent–hex edges and diketone additions on hex–hex edges. A particularly important stable structure is the mixed ether/ketone isomer of C 60O 6 in which a hinged C 5O 2 hatch lid containing two ketone oxygen atoms is opened revealing a hatch 4–5 Å in diameter. An even larger hole of approximately 6 Å in diameter is opened up in a particularly stable isomer of C 60O 9 which contains three ether and six ketone groups. Removal of the oxygen atoms from these structures and reoptimisation leads to hatch closing and C 60 is reformed.

A semiempirical study of the optimized ground and excited state potential energy surfaces of retinal and its protonated Schiff base

The electronic ground and first excited states of retinal and its Schiff base are optimized for the first time using the semiempirical AM1 Hamiltonian. The barrier for rotation about the C 11–C 12 double bond is characterized by variation of both the twist angle δ(C 10–C 11–C 12–C 13) and the bond length d(C 11–C 12). The potential energy surface is obtained by varying these two parameters. The calculated ground state rotational barrier is equal to 15.6 kcal/mol for retinal and 20.5 kcal/mol for its Schiff base. The all- trans conformation is more stable by 3.7 kcal/mol than the 11- cis geometry. For the first excited state, S 1, the 90° twisted geometry represents a saddle point for retinal with the rotational barrier of 14.6 kcal/mol. In contrast, this conformation is an energy minimum for the Schiff base. It can be easily reached at room temperature from the planar minima since it is separated from them by a barrier of only 0.6 kcal/mol. The 90° minimum conformation is more stable than the all- trans by 8.6 kcal/mol. We are thus able to present a reaction path on the S 1 surface of the retinal Schiff base with an almost barrierless geometrical relaxation into a twisted minimum geometry, as observed experimentally. The character of the ground and first excited singlet states underscores the need for the inclusion of double excitations in the calculations.

Structures and isomerism in C 70X 36, X=H, F. A comparison with C 60X 36

The structures and stabilities of isomers of C 70H 36 and C 70F 36 have been investigated using the AM1 Hamiltonian and the program MOPAC 6.0. There are many structurally related isomers of similar stability. All these isomers have ten bare carbon atoms in the equatorial plane of the molecule separating two C 30 hemispheres which do not interact strongly with each other. Each hemisphere contains 18 hydrogen atoms and six pairs of unhydrogenated carbon atoms which are isolated CC units or part of isolated C 6 units, these being separated by CH or CF groups. There are 62 possible hemispheres of which 51 exist as an optically active pair. Each hemisphere can be rotated relative to the other hemisphere by 72, 144, 216 or 288° leading to a large number of related structures. For C 70H 36 the stable isomers are constructed from only three types of hemisphere, labeled L, Aa and Ea, with two, two and one C 6 unit, respectively. There are two similarities between the most stable isomers of C 60X 36 and C 70X 36. Firstly, both contain a tetrahedral arrangement of four C 6 units, which in C 60X 36 form a regular tetrahedron and in C 70X 36 are as close to a regular tetrahedron as possible within the constraints of the C 70 skeleton. Secondly, in both C 60X 36 and C 70X 36 the 36 X atoms are distributed on twelve 1,2,3-C 5X 3 faces. Factors effecting the separation and characterization of C 70X 36 isomers are discussed.

Structures of C 70X 38 and C 70X 40, X=H,F

The structures and stabilities of C 70X 38 and C 70X 40 have been investigated using the AM1 Hamiltonian and the program MOPAC 6.0. Very similar results are obtained for X=H and F. As in C 70F 36, structures are based on an equatorial plane of 10 bare carbon atoms separating two C 30 hemispheres, which do not interact strongly with each other. Both hemispheres are C 30F 18 in C 70F 36, both C 30F 20 in C 70F 40 and there is one of each type in the intermediate C 70F 38. The unfluorinated carbon atoms are grouped as isolated C 6 rings or as isolated C 2 units. The C 30F 18 hemisphere used was the most stable hemisphere found previously for C 70F 36. All 120 possible C 30F 20 hemispheres were considered, 101 of which exist as a pair of optical isomers. Each hemisphere can be rotated relative to the other by 0, 72, 144, 216 or 288° relative to the other. Four C 30F 20 hemispheres were found to be more stable than the others, all of which contained one unfluorinated C 6 ring sharing an edge with the equatorial plane. For the most stable isomers, the 30 unfluorinated carbon atoms in C 70F 40 are grouped as two C 6 rings and nine CC units, compared with three C 6 and seven C 2 in C 70F 38, and four C 6 and five C 2 in C 70F 36. For each stoichiometry, however, there are many related structures of similar stability. A common feature of the most stable structures of C 70F 36, C 70F 38, and C 70F 40 is the presence of an unfluorinated C 6 ring attached to each side of the unfluorinated equatorial plane, the fluorine atoms being concentrated on the most curved parts of the molecules, which are most suited to tetrahedral carbon atoms.

Stereochemical patterns in [76] fullerenes, C 76H 30 to C 76H 44

The structures and stabilities of C 76H n as n increases from 28 to 44 have been calculated using the AM1 Hamiltonian and the program mopac 6.0. The structure of C 76H 28 consists of two C 14H 14 strings on the two most curved parts of the molecule, these strings being separated by relatively flat areas in which the carbon atoms are at the junction of three six-membered rings. Further addition of hydrogen to C 76H 28 does not extend the length of these strings but forms bridges between the two strings. These bridges can be CH–CH links on hex–hex edges, two different types of para-C 6H 2 links, or, for higher values of n, C 6H 4 links. The number of links increases as n increases, reaching five for C 76H 38, C 76H 40, C 76H 42 and C 76H 44. Apart from the exceptional cases of C 76H 30 and C 76H 44 there are several isomers of comparable stability for each stoichiometry.

QUANTITATIVE AND QUALITATIVE ANALYSIS OF COMPLEX DIELECTRIC PERMITTIVITY OF THE FERROELECTRIC LIQUID CRYSTAL ON THE BASIS OF THE NORDIO-RIGATTI-SEGRE THEORY

This paper presents the results of broadband dielectric studies of the dielectric relaxation of a macroscopically oriented ferroelectric liquid crystal. The Nordio-Rigatti-Segre theory is used to calculate some dielectric values and to compare with the experimental results. However, a few essential values have been calculated previously using the quantum chemical program MOPAC/7, with the AM1 Hamiltonian.

Structures and stabilities of adducts of carbenes and fullerenes, C 60(CR 2) n, R=H, CH 3, C 4H 9 and n=1–6

The addition of carbenes to C 60 to form C 60(CR 2) n , where R=H, CH 3, tert-C 4H 9 and n=1–6 has been investigated using the AM1 Hamiltonian and the program mopac 6.0. Addition to a carbon–carbon bond can be at a polyhedral edge shared between a C 5 and a C 6 ring, the pent–hex edge, or to an edge shared between two C 6 rings, the hex–hex edge. In each case the edge carbon–carbon bond can remain intact or be broken. Different behaviour is observed for the addition of CH 2, C(CH 3) 2 and C(C 4H 9) 2. The most important types of addition lead to the formation of pent–hex bond broken isomers and hex–hex bond intact isomers. The hex–hex bond broken isomer, however, exists as a local energy minimum for C 60(CH 2) n , n=1, 2, 3 and C 60[C(CH 3) 2] n , n=2, 3, and the pent–hex bond intact isomer is a local energy minimum for C 60[C(C 4H 9) 2]. Successive addition of CH 2 groups results in a clustering together of these groups with an opening out of a hole in the structure. Addition of successive C(CH 3) 2 groups or C(C 4H 9) 2 groups leads to structures in which these groups are well separated from each other and may be on pent–hex or hex–hex edges for C(CH 3) 2, or hex–hex edges for C(C 4H 9) 2.

Stereochemical patterns in [76]fullerenes, C 76 to C 76H 28

The structures and stabilities of C 76 and various isomers of C 76H n as n increases from 2 to 28 have been calculated using the AM1 Hamiltonian and the program mopac 6.0. C 76 forms an elongated structure with relatively flat areas in which some carbon atoms are at the junction of three six-membered rings. The bonding in some of these graphite-type rings is delocalised whereas in the remainder of the structure the double bonds are localised on edges linking two hexagonal faces. Hydrogenation occurs at these double bonds on the more curved part of the structure where each carbon atom is at the junction of one five-membered and two six-membered rings. The first stage of successive hydrogenations of this type leads to C 76H 20 in which there are two C 10H 10 zig-zag strings, each string formed by the edge sharing of four C 6H 4 rings. The second stage of hydrogenation leads to C 76H 28 in which these strings are extended by the hydrogenation of pent–hex edges. The stereochemical pattern is determined by the instability of CH groups on the triple hexagonal junctions, the localisation of double bonds on pent–hex edges, and the formation of C 6H 6 rings.

Langmuir-Blodgett films and optical second-harmonic generation of a crowned [60]fulleropyrrolidine

The Langmuir and Langmuir-Blodgett (LB) films of a novel crowned [60]fullero-pyrrolidine (CFP) were produced in different conditions. Macroscopic second-harmonic generation of the LB film was investigated by means of AM1 Hamiltonian as well as experiments. The monolayer LB film displayed a periodic fringe pattern. A linear dependence of second-harmonic intensity on the number of layers was observed. The second-order molecular susceptibility chi((2)) and hyperpolarizability beta were evaluated to be 3.2 x 10(-8) and 8.3 x 10(-29) esu.

Langmuir–Blodgett films and optical second-harmonic generation of a crowned [60]fulleropyrrolidine

The Langmuir and Langmuir–Blodgett (LB) films of a novel crowned [60]fullero-pyrrolidine(CFP) were produced in different conditions. Macroscopic second-harmonic generation of the LB film was investigated by means of AM1 Hamiltonian as well as experiments. The monolayer LB film displayed a periodic fringe pattern. A linear dependence of second-harmonic intensity on the number of layers was observed. The second-order molecular susceptibility χ(2) and hyperpolarizability β were evaluated to be 3.2×10−8 and 8.3×10−29esu.