From owner-chemistry@ccl.net Sun Nov 11 08:19:00 2007 From: "akef afaneh akef_afnh:-:yahoo.com" To: CCL Subject: CCL: To Whom it may Concern Message-Id: <-35579-071111081756-16708-IT5yU+aQlyxYptlx98PlNA_-_server.ccl.net> X-Original-From: akef afaneh Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-79924174-1194787062=:70861" Date: Sun, 11 Nov 2007 05:17:42 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: akef afaneh [akef_afnh\a/yahoo.com] --0-79924174-1194787062=:70861 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Quantum chemistry requires the solution of the time-independent Schrodinger equation, Hψ=Eψ where H is the Hamiltonian operator, ψ(R1, R2 . . . RN, r1, r2 . . . rn) is the wavefunction for all of the nuclei and electrons, and E is the energy associated with this wavefunction. The Hamiltonian contains all operators that describe the kinetic and potential energy of the molecule at hand. The wavefunction is a function of the nuclear positions R and the electron positions r. For molecular systems of interest to organic chemists, the Schrodinger equation cannot be solved exactly and so a number of approximations are required to make the mathematics tractable. The Born-Oppenheimer Approximation is the assumption that the electronic motion and the nuclear motion in molecules can be separated. It leads to a molecular wave function in terms of electron positions and nuclear positions . ψmolecule(ri,Rj)= ψelectron(ri,Rj) ψnuclei(Rj) This involves the following assumptions The electronic wavefunction depends upon the nuclear positions Rj but not upon their velocities, i.e., the nuclear motion is so much slower than electron motion that they can be considered to be fixed. The nuclear motion (e.g., rotation, vibration) sees a smeared out potential from the speedy electrons. In Hartree-Fock (HF) theory, the energy of a system is given as a sum of five components: EHF = ENN + ET + Ev + Ecoul + Eexch The nuclear-nuclear repulsion ENN describes the electrostatic repulsion between the nuclei and is independent of the electron coordinates. In time-independent HF theory, the kinetic energy of the nuclei is not, but the kinetic energy of the electrons ET is considered. Together with the nuclear-electron attraction energy Ev it depends on the coordinates of one electron. The classical electron-electron Coulomb repulsion energy Ecoul and the non-classical electron-electron exchange energy Eexch depend on the coordinates of two electrons. Calculation of these last two terms constitutes the main effort in HF calculations and is also responsible for the unfavorable formal scaling of computational effort as the fourth power of basis functions used for the description of the wavefunction. The particular assumption made in HF theory is that each electron feels the other electrons only as an average charge cloud, but not as individual electrons. The molecular electronic wavefunction in HF theory is based on the LCAO (=linear combination of atomic orbitals) scheme describing each molecular orbital (holding one electron) as a linear combination of basis functions (usually located at the nuclear center): Φi = ∑cµiχµ Where; Φi molecular orbital i cµi molecular orbital coefficient and χµ basis fuction The molecular orbital coefficients describe the contribution of each of the basis functions to a given molecular orbital. The overall electronic wavefunction of the system is constructed as an antisymmetrized product of the molecular orbitals (the Slater determinand) in order to fulfill the Pauli exclusion principle. Since the optimal shape of one molecular orbital depends on the shape of all the other occupied molecular orbitals, the optimization of the overall wavefunction is achieved in an iterative manner, varying the molecular orbital coefficients until no further changes in the overall wavefunction occur. The direction of the variation of MO coefficients is guided by the variational principle stating that an approximate wavefunction yields an energy of the system which is higher than the energy obtained from the exact wavefunction. In other words: in order to arrive at the most favorable wavefunction the MO coefficients must be varied such that the energy of the system becomes as low as possible. In Hartree-Fock calculations on closed shell systems (even number of electrons, all electrons paired) the electrons of opposite spin (spin-up, alpha vs. spin-down, beta) occupy the same spatial orbitals. The restriction of using the same spatial orbitals is usually reflected in the acronym RHF (=restricted Hartree-Fock) for these types of calculations. Once the numbers of alpha and beta spin electrons become different, however, this is not necessarily the best solution. If the restriction of identical spatial orbitals is retained in this situation, the method is called ROHF (Restricted Open Shell Hartree-Fock). If alpha and beta spin electrons are allowed to occupy different spatial orbitals the method is referred to as UHF (Unrestricted Hartree-Fock) method. While UHF calculations on open shell systems usually give lower energies and a better description of the unpaired electron density distribution (and thus EPR spectra), the UHF wavefunction is not an eigenfunction of the operator. In particular for spin-delocalized systems such as allylic or benzylic radicals, the UHF wavefunction can deviate substantially from that for a doublet state. The degree of deviation can be characterized through the difference between the expectation value of the operator (given after the SCF convergence note in the output file) and the value of S(S+1) for the current spin quantum number of the system. For a doublet state S=0.5 and S(S+1) = 0.750. In density functional theory (DFT) the energy of a system is given as a sum of six components: EDFT = ENN + ET + Ev + Ecoul + Eexch + Ecorr The definitions for the nuclear-nuclear repulsion ENN, the nuclear-electron attraction Ev, and the classical electron-electron Coulomb repulsion Ecoul energies are the same as those used in Hartree-Fock theory. The kinetic energy of the electrons ET as well as the non-classical electron-electron exchange energies Eexch are, however, different from those used in Hartree-Fock theory. The last term Ecorr describes the correlated movement of electrons of different spin and is not accounted for in Hartree-Fock theory. Due to these differences, the exchange energies calculated exactly in Hartree-Fock theory cannot be used in density functional theory. Various approaches exist to calculate the exchange and correlation energy terms in DFT methods. These approaches differ in using either only the electron density (local methods) or the electron density as well as its gradients (gradient corrected methods or generalized gradient approximation, GGA). Aside from these "pure" DFT methods, another group of hybrid functionals exists, in which mixtures of DFT and Hartree-Fock exchange energies are used. 1) Local methods Combination with the local VWN correlation functional by Vosko, Wilk and Nusair gives the Local Density Approximation (LDA) method. For open shell systems, using unrestricted wavefunctions, this is also referred to as the Local Spin Density Approximation (LSDA). This method is used with either the LSDA or SVWN keyword. 2) Gradient corrected methods The gradient-corrected exchange functionals include (given with their abbreviations in parenthesis): Becke88 (B) Perdew-Wang (PW91) Modified Perdew-Wang by Barone and Adamo (MPW) Gill96 (G96) Perdew-Burke-Ernzerhof (PBE) and the gradient-corrected correlation functionals are LYP by Lee, Yang, and Parr (LYP) Perdew-Wang (PW91) Perdew 86 (P86) Becke96 (B96) Perdew-Burke-Ernzerhof (PBE) In all cases, the names of these functionals refer to their respective authors and the year of publication. All combinations of exchange and correlation functionals are possible, the keywords being composed of the acronyms for the two functionals. The frequently used BLYP method, for example, combines Becke's 1988 exchange functional with the correlation functional by Lee, Yang, and Parr. Another frequently used GGA functional is BP86 composed of the Becke 1988 exchange functional and the Perdew 86 correlation functional. The PW91 functional combines exchange and correlation functionals developed by the same authors in 1991. 3) Hybrid functionals The basic idea behind the hybrid functionals is to mix exchange energies calculated in an exact (Hartree-Fock-like) manner with those obtained from DFT methods in order to improve performance. Frequently used methods are: Becke-Half-and-Half-LYP (BHandHLYP) uses a 1:1 mixture of DFT and exact exchange energies: EXC = 0.5*EX(HF) + 0.5*EX(B88) + EC(LYP) Becke-3-LYP (B3LYP) uses a different mixing scheme involving three mixing parameters: EXC = 0.2*EX(HF) + 0.8*EX(LSDA) + 0.72*DEX(B88) + 0.81*EC(LYP) + 0.19*EC(VWN) In this latter case, the B88 gradient correction to the local LSDA exchange energies carries its own scaling factor of 0.72. The three scaling factors have been derived through fitting the parameters to a set of thermochemical data (G1 set). PBE0 uses a 1:3 mixture of DFT and exact exchange energies: EXC = 0.25*EX(HF) + 0.75*EX(PBE) + EC(mPW91) B98 (Becke98) is based on a 10-parameter equation scaling components of exact exchange, GGA exchange and GGA correlation. All parameters have been optimized simultaneously to fit thermochemica data collected in the extended G2 data set: EXC = 0.2198*EX(HF) + EX + EC The Becke-half-and-half-LYP method is used with the BHandHLYP keyword, the very popular Becke-3-LYP method is used with the B3LYP keyword, and the PBE0 method with the PBE1PBE keyword. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com --0-79924174-1194787062=:70861 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Quantum chemistry requires the solution of the time-independent Schrodinger equation,
Hψ=Eψ
where H is the Hamiltonian operator, ψ(R1, R2 . . . RN, r1, r2 . . . rn) is the wavefunction for all of the nuclei and electrons, and E is the energy associated with this wavefunction. The Hamiltonian contains all operators that describe the kinetic and potential energy of the molecule at hand. The wavefunction is a function of the nuclear positions R and the electron positions r. For molecular systems of interest to organic chemists, the Schrodinger equation cannot be solved exactly and so a number of approximations are required to make the mathematics tractable.
 
The Born-Oppenheimer Approximation is the assumption that the electronic motion and the nuclear motion in molecules can be separated. It leads to a molecular wave function in terms of electron positions and nuclear positions .
ψmolecule(ri,Rj)= ψelectron(ri,Rj) ψnuclei(Rj)
This involves the following assumptions
  • The electronic wavefunction depends upon the nuclear positions Rj but not upon their velocities, i.e., the nuclear motion is so much slower than electron motion that they can be considered to be fixed.
  • The nuclear motion (e.g., rotation, vibration) sees a smeared out potential from the speedy electrons.
 
In Hartree-Fock (HF) theory, the energy of a system is given as a sum of five components:

EHF = ENN + ET + Ev + Ecoul + Eexch

The nuclear-nuclear repulsion ENN describes the electrostatic repulsion between the nuclei and is independent of the electron coordinates. In time-independent HF theory, the kinetic energy of the nuclei is not, but the kinetic energy of the electrons ET is considered. Together with the nuclear-electron attraction energy Ev it depends on the coordinates of one electron. The classical electron-electron Coulomb repulsion energy Ecoul and the non-classical electron-electron exchange energy Eexch depend on the coordinates of two electrons. Calculation of these last two terms constitutes the main effort in HF calculations and is also responsible for the unfavorable formal scaling of computational effort as the fourth power of basis functions used for the description of the wavefunction. The particular assumption made in HF theory is that each electron feels the other electrons only as an average charge cloud, but not as individual electrons.

The molecular electronic wavefunction in HF theory is based on the LCAO (=linear combination of atomic orbitals) scheme describing each molecular orbital (holding one electron) as a linear combination of basis functions (usually located at the nuclear center):
Φi = ∑cµiχµ
Where; Φi molecular orbital i
             cµi molecular orbital coefficient
      and χµ basis fuction

The molecular orbital coefficients describe the contribution of each of the basis functions to a given molecular orbital. The overall electronic wavefunction of the system is constructed as an antisymmetrized product of the molecular orbitals (the Slater determinand) in order to fulfill the Pauli exclusion principle. Since the optimal shape of one molecular orbital depends on the shape of all the other occupied molecular orbitals, the optimization of the overall wavefunction is achieved in an iterative manner, varying the molecular orbital coefficients until no further changes in the overall wavefunction occur. The direction of the variation of MO coefficients is guided by the variational principle stating that an approximate wavefunction yields an energy of the system which is higher than the energy obtained from the exact wavefunction. In other words: in order to arrive at the most favorable wavefunction the MO coefficients must be varied such that the energy of the system becomes as low as possible.
In Hartree-Fock calculations on closed shell systems (even number of electrons, all electrons paired) the electrons of opposite spin (spin-up, alpha vs. spin-down, beta) occupy the same spatial orbitals. The restriction of using the same spatial orbitals is usually reflected in the acronym RHF (=restricted Hartree-Fock) for these types of calculations. Once the numbers of alpha and beta spin electrons become different, however, this is not necessarily the best solution. If the restriction of identical spatial orbitals is retained in this situation, the method is called ROHF (Restricted Open Shell Hartree-Fock). If alpha and beta spin electrons are allowed to occupy different spatial orbitals the method is referred to as UHF (Unrestricted Hartree-Fock) method.
While UHF calculations on open shell systems usually give lower energies and a better description of the unpaired electron density distribution (and thus EPR spectra), the UHF wavefunction is not an eigenfunction of the <S2> operator. In particular for spin-delocalized systems such as allylic or benzylic radicals, the UHF wavefunction can deviate substantially from that for a doublet state. The degree of deviation can be characterized through the difference between the expectation value of the <S2> operator (given after the SCF convergence note in the output file) and the value of S(S+1) for the current spin quantum number of the system. For a doublet state S=0.5 and S(S+1) = 0.750.
In density functional theory (DFT) the energy of a system is given as a sum of six components:
EDFT = ENN + ET + Ev + Ecoul + Eexch + Ecorr

The definitions for the nuclear-nuclear repulsion ENN, the nuclear-electron attraction Ev, and the classical electron-electron Coulomb repulsion Ecoul energies are the same as those used in Hartree-Fock theory. The kinetic energy of the electrons ET as well as the non-classical electron-electron exchange energies Eexch are, however, different from those used in Hartree-Fock theory. The last term Ecorr describes the correlated movement of electrons of different spin and is not accounted for in Hartree-Fock theory. Due to these differences, the exchange energies calculated exactly in Hartree-Fock theory cannot be used in density functional theory.

Various approaches exist to calculate the exchange and correlation energy terms in DFT methods. These approaches differ in using either only the electron density (local methods) or the electron density as well as its gradients (gradient corrected methods or generalized gradient approximation, GGA). Aside from these "pure" DFT methods, another group of hybrid functionals exists, in which mixtures of DFT and Hartree-Fock exchange energies are used.

1) Local methods

Combination with the local VWN correlation functional by Vosko, Wilk and Nusair gives the Local Density Approximation (LDA) method. For open shell systems, using unrestricted wavefunctions, this is also referred to as the Local Spin Density Approximation (LSDA). This method is used with either the LSDA or SVWN keyword.

2) Gradient corrected methods

The gradient-corrected exchange functionals include (given with their abbreviations in parenthesis):
  • Becke88 (B)
  • Perdew-Wang (PW91)
  • Modified Perdew-Wang by Barone and Adamo (MPW)
  • Gill96 (G96)
  • Perdew-Burke-Ernzerhof (PBE)
and the gradient-corrected correlation functionals are
  • LYP by Lee, Yang, and Parr (LYP)
  • Perdew-Wang (PW91)
  • Perdew 86 (P86)
  • Becke96 (B96)
  • Perdew-Burke-Ernzerhof (PBE)
In all cases, the names of these functionals refer to their respective authors and the year of publication. All combinations of exchange and correlation functionals are possible, the keywords being composed of the acronyms for the two functionals. The frequently used BLYP method, for example, combines Becke's 1988 exchange functional with the correlation functional by Lee, Yang, and Parr.

Another frequently used GGA functional is BP86 composed of the Becke 1988 exchange functional and the Perdew 86 correlation functional. The PW91 functional combines exchange and correlation functionals developed by the same authors in 1991.

3) Hybrid functionals

The basic idea behind the hybrid functionals is to mix exchange energies calculated in an exact (Hartree-Fock-like) manner with those obtained from DFT methods in order to improve performance. Frequently used methods are:
  • Becke-Half-and-Half-LYP (BHandHLYP) uses a 1:1 mixture of DFT and exact exchange energies:
    EXC = 0.5*EX(HF) + 0.5*EX(B88) + EC(LYP)
  • Becke-3-LYP (B3LYP) uses a different mixing scheme involving three mixing parameters:
EXC = 0.2*EX(HF) + 0.8*EX(LSDA) + 0.72*DEX(B88) + 0.81*EC(LYP) + 0.19*EC(VWN)
In this latter case, the B88 gradient correction to the local LSDA exchange energies carries its own scaling factor of 0.72. The three scaling factors have been derived through fitting the parameters to a set of thermochemical data (G1 set).
  • PBE0 uses a 1:3 mixture of DFT and exact exchange energies:
    EXC = 0.25*EX(HF) + 0.75*EX(PBE) + EC(mPW91)
  • B98 (Becke98) is based on a 10-parameter equation scaling components of exact exchange, GGA exchange and GGA correlation. All parameters have been optimized simultaneously to fit thermochemica data collected in the extended G2 data set:
    EXC = 0.2198*EX(HF) + EX + EC
The Becke-half-and-half-LYP method is used with the BHandHLYP keyword, the very popular Becke-3-LYP method is used with the B3LYP keyword, and the PBE0 method with the PBE1PBE keyword.

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http://mail.yahoo.com --0-79924174-1194787062=:70861-- From owner-chemistry@ccl.net Sun Nov 11 13:11:01 2007 From: "Bryan Bishop kanzure[]gmail.com" To: CCL Subject: CCL: To Whom it may Concern Message-Id: <-35580-071111103654-29229-wVy+niNOuqFBnw2vsON/jQ ~~ server.ccl.net> X-Original-From: Bryan Bishop Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="utf-8" Date: Sun, 11 Nov 2007 08:33:56 -0600 MIME-Version: 1.0 Sent to CCL by: Bryan Bishop [kanzure(-)gmail.com] On Sunday 11 November 2007 07:17, akef_afnh:-:yahoo.com wrote: > Quantum chemistry requires the solution of the time-independent > Schrodinger equation, Hψ=Eψ > where H is the Hamiltonian operator, ψ(R1, R2 . . . RN, r1, r2 Hello. The formatting on the email impedes its reading. Can we fix this? - Bryan From owner-chemistry@ccl.net Sun Nov 11 18:38:00 2007 From: "Randall H Goldsmith r-goldsmith _ northwestern.edu" To: CCL Subject: CCL:G: NBO Natural Bond Orbital Deletion Gaussian 98 Message-Id: <-35581-071111132725-12350-3Bgv28Vz/0h018aNY8dyaA : server.ccl.net> X-Original-From: "Randall H Goldsmith" Date: Sun, 11 Nov 2007 13:27:21 -0500 Sent to CCL by: "Randall H Goldsmith" [r-goldsmith^^northwestern.edu] Hello all, I'm looking to perform NBO deletion analysis using the NBO 3.1 package that comes with Gaussian 98. Following instructions for NBO 3.0 implementation in Gaussian 88 (the only ones i can find), i attempted to use nonstandard input to tell Gaussian to do the analysis, but the job always died prematurely. Does anybody know how to perform this analysis in Gaussian 98? Obviously, an example job file would be most valuable. Thank you very much for your time! randall. From owner-chemistry@ccl.net Sun Nov 11 21:49:00 2007 From: "Praveen Kumar Shrivastava praveenshrivastav[A]gmail.com" To: CCL Subject: CCL: Hydrogen bond and QSAR Message-Id: <-35582-071111195701-11287-0ty7gEKGZISni6/EAg+nZw^^^server.ccl.net> X-Original-From: "Praveen Kumar Shrivastava" Date: Sun, 11 Nov 2007 19:56:56 -0500 Sent to CCL by: "Praveen Kumar Shrivastava" [praveenshrivastav ~ gmail.com] Hello all, Two different drug molecule joined by hydrogen bond can be analysed for QSAR methodlogy considering as one molecule. Thank you very much for your time! Praveen From owner-chemistry@ccl.net Sun Nov 11 22:23:01 2007 From: "Yangsoo Kim vsmember..gmail.com" To: CCL Subject: CCL: Looking for Point Group Symmetrizing Program Message-Id: <-35583-071111215528-18443-R6JHXCXeuJQIGKrTkF2gdg++server.ccl.net> X-Original-From: "Yangsoo Kim" Content-Type: multipart/alternative; boundary="----=_Part_12075_26750964.1194832710815" Date: Mon, 12 Nov 2007 10:58:30 +0900 MIME-Version: 1.0 Sent to CCL by: "Yangsoo Kim" [vsmember(~)gmail.com] ------=_Part_12075_26750964.1194832710815 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear CCL Members, I'm looking for a program that can change into molecular coordinates having higher-order point group. The purpose of that program is the fine tuning of input coordinates. Then I found the symmetrize tool (Enable Point Group Symmetry) in Gaussview3. But I want to execute in command mode, not GUI... I would appreciate if you could give me some suggestions. Thank you very much. Yangsoo Kim ------=_Part_12075_26750964.1194832710815 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline

Dear CCL Members,

I'm looking for a program that can change into molecular coordinates having higher-order point group.
The purpose of that program is the fine tuning of input coordinates.
Then I found the symmetrize tool (Enable Point Group Symmetry) in Gaussview3.
But I want to execute in command mode, not GUI...

I would appreciate if you could give me some suggestions.
Thank you very much.


Yangsoo Kim

------=_Part_12075_26750964.1194832710815--