AM1 calculations for compounds containing silicon

Dewar, Michael J. S.; Jie, Caoxian

doi:10.1021/om00150a020

Cited by 110 publications

(32 citation statements)

References 2 publications

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“…12,13 The semiempirical Austin method (AM1) [11][12][13] used in this study calculates the most probable geometries of specific molecules submitted to the program by solving Schrö dinger's equation (H = E) for all valence electrons in the molecule. In this equation, H is the Hamiltonian operator, E represents the eigenvalues, and is the wavefunction.…”

Section: Molecular Modeling: Molecular Orbital Methodsmentioning

confidence: 99%

Molecular modeling study of adsorption of poly-L-lysine onto silica glass

West

Latour

Hench

1997

J. Biomed. Mater. Res.

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A research program was initiated with both experimental and computational chemistry based molecular modeling components to investigate specific amino acid-surface interactions. The experimental portion of this study, with details reported elsewhere, investigated the adsorption of selected molecular weights of poly(L-lysine) onto silica glass microspheres with the adsorption enthalpy per adsorbed mer determined to be -0.23 +/- 0.13 kcal/mol (mean +/- 95% confidence interval). Molecular modeling of this system was then conducted using two approaches: an AM1 semiempirical molecular orbital method to predict L-lysine/glass interaction energy and an MM2 molecular mechanics method to investigate the structural configuration for poly(L-lysine). The modeling predicted a minimum energy configuration of a rotational backbone structure for poly(L-lysine) with approximately one full rotation occurring about every 8 mers, and that the amine side chains of the L-lysine will hydrogen bond with the silica surface with an average adsorption energy of approximately -0.34 kcal/mol/mer. The molecular modeling results are in good agreement with the experimentally measured value and provide insights into possible molecular-level behavior which would be very difficult to determine by experimental analyses alone. This work demonstrates the use of molecular modeling in conjunction with experimental studies to investigate complex molecular interactions.

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Section: Molecular Modeling: Molecular Orbital Methodsmentioning

confidence: 99%

Molecular modeling study of adsorption of poly-L-lysine onto silica glass

West

Latour

Hench

1997

J. Biomed. Mater. Res.

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“…Thus, it was considered necessary to continue the investigation of the orbital structure of 1. In this paper we have analyzed the PE spectra of compounds 2-7 and 1-methyl-2-carbasilatrane, CHHSi(OCH2CH2)2(CH2CH2CH2)N (8) as well as the results of quantum chemical (MNDO [11], AM1 [12]) calculations of the molecules 2, 3, 7, 8, and 1-methoxysilatrane (6a), a simpler analogue of 6. See Scheme 1.…”

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confidence: 99%

Photoelectron spectra and orbital structures of silatranes: Organic derivatives of pentacoordinate silicon

Sidorkin

Balakhchi

1994

Struct Chem

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The photoelectron (PE) spectra of silatranes (1), 2,8,9-trioxa-5-aza-l-silabicyclo [3.3.3] undecanes, have been analyzed and partially reinvestigated. In the PE spectra of 1 the bands in the 8.2-8.9 eV region, which were previously ascribed to the lone electron pair (LEP) orbital of the nitrogen atom or the SiN bond, are due to the presence of impurities, the products of incomplete hydrolysis. Interpretation of the bands in the PE spectra of pure compounds was carded out by analysis of orbital-correlation diagrams and results of MNDO and AM 1 calculations. The first ionization potential of 1 is associated with a MO localized to a great extent on the axial X--S i--N fragment. The increase with shortening of the Si--N distance is related to the corresponding increase in the degree of noncoplanarity of the nitrogen atom when its LEP is involved in the hypervalent X--Si--N bond.KEY WORDS: Photoelectron spectra; silatranes; orbital-correlation diagram. ~TRODUCTIONSilatranes, XSi (OCHRCH2)3N (1), hold a special position among organic derivatives of pentacoordinate silicon (and its subgroup elements). It is the investigation of their physicochemical properties that has been revealed the most general signs of expansion of the silicon coordination number [1][2][3]. Nevertheless, the main question concerning the orbital structure of 1 remains in dispute. Thus, an empirical assignment of the PE bands of 1-methyl-, 1-hydro-, and 1-ethoxysilatranes turns out to be ambiguous and leads to alternative versions for orbital interactions in such molecules [4]. Subsequent studies of the PE spectra of 1-methylsilatrane, its 3,7,10-trimethylderivative and 1-methyl-2-carbasilatrane as well as a number of model 2-aklanolamines and their O-silylated analogues have made the question of the orbital structure of 1 even more complicated. Initially, the first maximum (8.5 eV) in the PE spectrum of 'Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia. 2 Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 664033 Irkutsk, Russia. 1891-methylsilatrane was assigned to the presence of an impurity [5], but subsequently to the nitrogen electron pair of the silatrane molecule in an unusual (and unknown) conformation [6]. Recently the PE spectra of a large series of silatranes were interpreted to a great extent on the basis of ab initio STO-3G calculations of 1-methyl-, 1-fluoro-, 1-chloro-, 1-vinyl-, and 1-chloromethylsilatrane [7]. In this study, however, no account was taken of the experimentally confirmed significant substituent effect on the Si--N bond length of 1-substituted silatranes, nor the pronounced difference of its values in the crystalline and gaseous phase [8,9]. These calculations were carded out without geometry optimization using the same SiN distance for all molecules, which was taken from the X-ray study of 1-methylsilatrane. Therefore, the suggested assignment of the bands in the PE spectra of 1 [7] does not seem to be convincing. This is expressed, in particular...

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“…The MNDO method also overestimates transition-state energies and distorts transition-state geometries, again fatal flaws for calculating bond fracture mechanisms. The Austin Method (AM1), 7,15,17 also a semi-empirical method, reduces these problems by modifying the core repulsion function used in MNDO with additional Gaussian terms, and the calculated structures and heats of formation match quite well with experimental values. 18 We recently have shown that various sizes of silica rings calculated by either the AM1 or the PM3 method represent the geometries and infrared spectra better than previous MNDO IR spectra and geometries.…”

Section: Molecular Orbital (Mo) Methodsmentioning

confidence: 99%

Theoretical analysis of hydrolysis of polydimethylsiloxane (PDMS)

West

1997

J. Biomed. Mater. Res.

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Silicones (polydimethylsiloxane, PDMS) are the materials currently used in most breast implants. ICP and FTIR analysis of the tissue capsule around aged breast implants and in vitro models show that Si-containing material is leaking from the PDMS implants. In this study, the hydrolysis of PDMS has been theoretically modeled using a semiempirical quantum mechanical method called AM1. The activation barrier for removing a methanol monomer was found to be +82 Kcal/mol while the removal of a methane monomer was +41 Kcal/mol. Using the same AM1 method, hydrolysis of the identical to Si-O-Si identical to bond also has been modeled for pentasilicic acid and, in this study, for 1,1,3,3,-fetramethyldisiloxane-1,3-diol. The barrier to the removal of a silicon-containing tetrahedron for both studies was found to be +27 Kcal/mol. This is approximately one and a half times smaller than the energy of that needed to remove a methyl group. The pentacoordinated silicon-activated transition state for hydrolysis of PDMS may provide an energetically favorable pathway for development of a surface that will enhance chemisorption of charged protein molecules, and such a pathway may show up in NMR studies of the hydrolysis of PDMS.

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AM1 calculations for compounds containing silicon

Cited by 110 publications

References 2 publications

Molecular modeling study of adsorption of poly-L-lysine onto silica glass

Molecular modeling study of adsorption of poly-L-lysine onto silica glass

Photoelectron spectra and orbital structures of silatranes: Organic derivatives of pentacoordinate silicon

Theoretical analysis of hydrolysis of polydimethylsiloxane (PDMS)

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