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WO1999050768A1 - Procede de calcul de proprietes de conformation structurale d'une grande molecule - Google Patents

Procede de calcul de proprietes de conformation structurale d'une grande molecule Download PDF

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Publication number
WO1999050768A1
WO1999050768A1 PCT/JP1998/001484 JP9801484W WO9950768A1 WO 1999050768 A1 WO1999050768 A1 WO 1999050768A1 JP 9801484 W JP9801484 W JP 9801484W WO 9950768 A1 WO9950768 A1 WO 9950768A1
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WIPO (PCT)
Prior art keywords
seoem
molecule
molecules
molecular
large molecule
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Ceased
Application number
PCT/JP1998/001484
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English (en)
Inventor
Gyula Tasi
Fujio Mizukami
Shu-Ichi Niwa
Makoto Toba
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National Institute of Advanced Industrial Science and Technology AIST
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Agency of Industrial Science and Technology
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Priority to PCT/JP1998/001484 priority Critical patent/WO1999050768A1/fr
Priority to JP54914499A priority patent/JP3353076B2/ja
Publication of WO1999050768A1 publication Critical patent/WO1999050768A1/fr
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

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    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
    • G16C20/00—Chemoinformatics, i.e. ICT specially adapted for the handling of physicochemical or structural data of chemical particles, elements, compounds or mixtures
    • G16C20/30—Prediction of properties of chemical compounds, compositions or mixtures
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
    • G16C10/00—Computational theoretical chemistry, i.e. ICT specially adapted for theoretical aspects of quantum chemistry, molecular mechanics, molecular dynamics or the like

Definitions

  • the present invention relates to a method of calculating structural conformational properties of large molecule.
  • the ZPVE and thermal energy corrections which are generally calculated from the vibrational frequencies, are not on the same scale as the calculated total energies. This means that these methods add the almost precise ZPVE and thermal energy corrections to the too small electronic energy to get the semiempirical total energy.
  • the AMI ZPVE correction of the neopentane molecule is 0.160068 heartree and the real value amounts to 0.152377 hartree. It is to be seen that in this case the AMI value closely matches the real one. For the total energies, this is not so: the AMI value is about 6.7 times smaller than the real value (see (2) above) .
  • the new quantum chemical method of this invention is called the scaled effective one-electron method (SEOEM) .
  • This quantum chemical method affords molecular total energies, in contrast to the current semiempirical or approximate methods, which are very close to the Gaussian-2 and to the experimental values.
  • the SEOEM model takes all the electrons in the system into consideration ("all electron-method").
  • the current semiempirical or approximate methods consider only the valence electrons.
  • the SEOEM model uses the atomic overlap integral matrix in its formalism.
  • the current semiempirical or approximate methods are ZDO models, that is they neglect the atomic overlap integral matrix.
  • Gaussian-2 molecular total energies (at 0 K) and zero- point vibrational energy corrections were used. Further important reference properties were the followings: ab initio molecular geometries and permanent electric dipole moments. In the parameterization for aliphatic alkanes, larger molecules with conformational flexibility were also involved.
  • the SEOEM model can be applied for conformational analysis of large molecules.
  • the results obtained for unbranched aliphatic alkanes show that this model can identity all the different conformers of a molecule on the molecular potential energy surface.
  • This model can also be applied for studying the thermodynamic properties of large molecules.
  • the method can be used at any temperature without the introduction of new parameters.
  • the results obtained for aliphatic alkanes show that it is important to perform full conformational analysis and to treat the hindered torsional vibrations as free internal rotations at room and higher temperatures.
  • Our reliable approximate quantum chemical method (formalism) can be applied to study the structural (conformational) , electronic and thermodynamic properties of large molecules. The reliability of an approximate method first of all depends on the theoretical background and on the quality of its parameterization.
  • thermodynamic properties can then be calculated after performing vibrational analysis. If we perform the parameterization in this manner, the molecular total energies, ZPVE and thermal energy corrections will be on the same scale.
  • Figure 1 is a graph showing the rmsd deviations of the equilibrium molecular geometries determined by various methods from the reference geometries.
  • Figure 2 is a graph showing the relation ⁇ (ref) vs ⁇ (SEOEM) for aliphatic alkanes.
  • Figure 3 is a diagram showing the fractions of different conformers of the nonane molecule at 298.15 K and at 1 atm.
  • Figure 4 is a diagram showing the standard heats of formation of the conformers of nonane.
  • Figure 5 is a graph showing the relation between the experimental and SEOEM I standard heats of formation for aliphatic alkanes (kJ/mol) .
  • Figure 6 is a graph showing the relation between the experimental and SEOEM II standard heats of formation for aliphatic alkanes (kJ/mol) .
  • Figure 7 is a graph showing the relation between the experimental and GAV standard heats of formation for aliphatic alkanes (kJ/mol) .
  • Figure 8 is a graph showing the relation between the experimental and AMI standard heats of formation for aliphatic alkanes (kJ/mol).
  • EHMO Extended H ⁇ ckel Molecular Orbital
  • A. B. Hoftmann, R. , J. Chem. Phys., 39, 1397 (1963), the disclosure of which is incorporated by reference.
  • ASD Atom Superposition and Electron Delocalization
  • Anderson A. B. Hoftmann R. , J. Chem. Phys., 60, 4271 (1974); Anderson A. B., J. Chem. Phys., 62, 1187 (1975); Anderson. A. B., J. Chem.
  • H is the matrix of the effective one-electron Hamiltonian
  • S is the overlap integral matrix of atomic orbitals
  • ⁇ is the energy of the MO defined by the column vector c of the MO expansion coefficients.
  • the elements of the effective one-electron matrix H are given by the well-known eqs 6 and 7 ([10,11] see supra. ) :
  • the matrix in eq 8 is the energy-weighted density matrix defined by eq 9:
  • R7B is the distance between atoms A and B.
  • parameters & ⁇ v > ⁇ v ani ⁇ ⁇ v are to be determined via parameter estimation.
  • the exponents of the atomic gaussian basis functions (GTO ⁇ Gaussian Type Orbital) play a role in the calculation of the matrix S. They determine the size of the atomic orbitals.
  • the scaling factors ( ⁇ ns anc *Cnp) °f tne GTOs are taken as parameters.
  • STO-3G basis set for aliphatic alkanes STO ⁇ Slater Type Orbital
  • the STO-3G designation means that a linear combination of 3 primitive gaussians is used to approximate every atomic orbital .
  • Z / .. and Z ⁇ are the atomic numbers (nuclear charges) of atoms A and B, respectively.
  • the atomic parameters ⁇ & , ⁇ - Q , ⁇ ⁇ and _g should be determined via parameter optimization.
  • the number of parameters to be adjusted is 21 for aliphatic alkanes.
  • the gradient vector V ⁇ E ot with respect to the coordinates of atom A can be calculated via eq 13, derived from eq 8:
  • the notation ⁇ GA means that the summation is carried out over the AOs centered on atom A.
  • FC frozen core
  • the parameterization of the SEOEM model was performed on the following basis set of molecules: methane, ethane, propane, butane (t), butane (g + ) , isobutane, pentane (tt) , pentane (g ⁇ t) , pentane (g ⁇ g ⁇ ) , pentane (g + g' + ) , isopentane and neopentane.
  • the reference properties were the RMP2 (FC) 6-311G** equilibrium molecular geometries, the RHF/6- 311++G**//RMP2 (FC/6-311G** permanent electric dipole moment vectors ( ⁇ (ref ) ) ([18] see supra.) and the G2 total energies at 0 K ( ⁇ E-tot ⁇ ( G ⁇ ) ) , including the zero- point vibrational energy (ZPVE(G2)) corrections.
  • the scaled HF/6-31G* harmonic vibrational frequencies are used to calculate the ZPVEs.
  • the value of the scale factor is 0.8929 ([19]: Pople, J. A.; Scott, A. P.; Wong, M. W.
  • Table 1 shows the reference data, together with the G2 enthalpies of formation at 0 K ( ⁇
  • thermodynamic properties first of all depends on the quality of the ZPVE and thermal energy corrections. Therefore, it is desirable to perform the parameterization at 0 K and to take the ZPVE corrections into consideration.
  • the gradient vector of the total energy with respect to the atomic coordinates is computed analytically by using eq 8.
  • the BFGS algorithm is used with some modifications ([24]: Thiel, W., J. Mol . Struct. 163, 415 (1988), the disclosure of which are incorporated by reference.).
  • normal-coordinate analysis can be performed.
  • the infrared absorption intensities can also be evaluated.
  • E rep i n ec 3- (3) can be calculated in several ways. It is possible to use the function defined in the original ASED method ([11] see supra.) and the function applied in the EHNDO method ([13] see supra.).
  • the second program is a general code for parameterization of a quantum chemical model, i.e. it provides the parameters for the SEHMO program. Only the following steps are necessary: (1) definition of the quantum chemical model, then (2) selection of the reference molecules and properties, and finally (3) choice of a trial parameter set. Much valuable experience has accumulated concerning the parameterization of semiempirical quantum chemical models ([3] see supra.). In preparing the PSEHMO program, we have made use of this experience.
  • Table 5 shows the statistical data ( ⁇ : regression coefficient, p : linear correlation coefficient, and ⁇ : root mean-square deviation) obtained by linear regression analyses between the reference and SEOEM data.
  • Figure 1 shows the deviations of the equilibrium molecular geometries obtained by various quantum chemical methods from the RMP2 (FC) /6-311G** geometries.
  • the rmsd (root mean-square distance) data were calculated via eq 14:
  • Figure 2 shows the correlation between the RHF/6- 311++G**//RMP2 (FC) /6-311G** and the SEOEM dipole moments It can be seen that the correlation is acceptably good.
  • Figure 1 shows the rmsd deviations (A) of the equilibrium molecular geometries determined by various methods from the reference geometries.
  • Table 6 shows gas-phase experimental and calculated standard heats of formation for 63 aliphatic alkane molecules.
  • the experimental values were obtained from a recent compilation (([29]: Cohen, N., J. Phys. Chem. Ref. Data, 25, 1411 (1996) 111, the disclosure of which is incorporated by reference.).
  • GAV group additivity values
  • Figure 2 shows the graphical representation of the relation ⁇ (ref) vs. ⁇ (SEOEM) for aliphatic alkanes (Debye).
  • Xj_ is the fraction of conformer i in the gas mixture at 298.15 K and at 1 atm. These fractions were calculated via eq 16 by assuming that Boltzmann statistics can be applied to determine the populations of different conformers:
  • ⁇ Ej_ is the difference between the energies of conformer i and the conformer with the lowest energy (global minimum).
  • ⁇ Hf i 298 the low-frequency torsional vibrations were regarded as free internal rotations.
  • the cut-off value used was 260 cm ⁇ l, as suggested by Radom et al. ([30]: Nicolaides,
  • Figures 3 and 4 show the results of the SEOEM conformational analysis. In this case, 1073 different conformers were found on the PES, and it can be stated that there are no conformers more for nonane. All the conformers are within 23 kJ/mol of the global minimum, which is "linear".
  • the SEOEM model can be applied for conformational analysis of large molecules.
  • the results obtained for unbranched aliphatic alkanes show that this model can identify all the different conformers of a molecule on the molecular potential energy surface.
  • Table 6 presents the standard heats of formation calculated for the conformers obtained from the global minima of the SEOEM potential energy surfaces via geometry optimization.
  • the AMI method tends to overestimate the stability of the "all-trans" conformer ([6] see supra.).
  • Figures 5-8 show the correlations between the experimental and calculated values.
  • Table 7 contains the statistical data ( ⁇ : regression coefficient, p: linear correlation coefficient, ⁇ : root mean-square deviation, AAD: average absolute deviation and MAD: maximum absolute deviation) obtained by linear regression analysis. It can be seen that the GAV and SEOEM II standard heats of formation are the best among the calculated values. It is worth noting, however, that the SEOEM model can be applied at any temperature without the introduction of new parameters. If we want to use the GAV method at a temperature which is different from the room temperature, we should derive new parameters.
  • the GAV method does not afford molecular geometries, electric dipole moments and other electronic properties .
  • the SEOEM model can be applied for studying the thermodynamic properties of large molecules.
  • the method can be used at any temperature.
  • the results obtained for aliphatic alkanes show that it is important to perform full conformational analysis and to treat the hindered torsional vibrations as free internal rotations at room and higher temperatures.
  • the new quantum chemical model is called the scaled effective one- electron method (SEOEM) .
  • SEOEM scaled effective one- electron method
  • the SEOEM model can be applied for large molecules and the required CPU time is very small comparing to that of the G2 calculations. For instance, only one G2 calculation on one conformer of the butane and pentane molecules takes 5.7 and 22.0 hours on a CRAY C90 computer, respectively. The SEOEM calculation takes only 2.1 and 4.5 seconds, respectively, on the same computer. It is to be seen that the SEOEM calculations can be performed even on a moderate cost PC machine or work station.
  • the SEOEM model can be applied for conformational analysis of large molecules.
  • the results obtained for unbranched aliphatic alkanes clearly show that, in contrast to the molecular mechanics and dynamics methods, this model can identify all the different conformers of a molecule on the potential energy surface.
  • a further possible industrial application area for the SEOEM model is the shape selective catalysis. In shape selective catalysis, the chemical transformation of a substance depends on its size and shape. If the substance has conformational flexibility, the SEOEM model can be applied to determine the structures

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  • Crystallography & Structural Chemistry (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
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  • Theoretical Computer Science (AREA)
  • Complex Calculations (AREA)
  • Organic Low-Molecular-Weight Compounds And Preparation Thereof (AREA)

Abstract

L'invention concerne un nouveau procédé de chimie quantique et de paramétrage. Pour calculer les énergies totales moléculaires fiables d'une grande molécule, qui sont proches des valeurs expérimentales réelles ou des valeurs initiales de qualité élevée, le procédé comporte les étapes consistant à accroître et paramétrer les potentiels d'ionisation des électrons de l'enveloppe interne du noyau atomique pour mettre en oeuvre la coïncidence des énergies totales dans une approximation efficace pour un électron, tout en prenant en compte tous les électrons de ladite molécule. Le procédé peut également être appliqué au calcul des propriétés thermodynamiques d'une grande molécule.
PCT/JP1998/001484 1998-03-31 1998-03-31 Procede de calcul de proprietes de conformation structurale d'une grande molecule Ceased WO1999050768A1 (fr)

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PCT/JP1998/001484 WO1999050768A1 (fr) 1998-03-31 1998-03-31 Procede de calcul de proprietes de conformation structurale d'une grande molecule
JP54914499A JP3353076B2 (ja) 1998-03-31 1998-03-31 大きな分子の構造的性質を計算する方法

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Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2001016810A3 (fr) * 1999-08-31 2002-05-02 European Molecular Biology Lab Embl Procede informatise destine a l'ingenierie et a la conception macromoleculaires

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
CURTISS L A ET AL: "Gaussian-2 theory for molecular energies of first- and second-row compounds", JOURNAL OF CHEMICAL PHYSICS, 1 JUNE 1991, USA, vol. 94, no. 11, ISSN 0021-9606, pages 7221 - 7230, XP002088959 *
TASI G ET AL: "A new program for effective one-electron (EHMO-ASED) calculations", COMPUTERS & CHEMISTRY, 1997, ELSEVIER, UK, vol. 21, no. 5, ISSN 0097-8485, pages 319 - 325, XP002088958 *

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2001016810A3 (fr) * 1999-08-31 2002-05-02 European Molecular Biology Lab Embl Procede informatise destine a l'ingenierie et a la conception macromoleculaires

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JP3353076B2 (ja) 2002-12-03

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