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Introduction
and number of quantum particles such as nuclei, muons, positrons and pseudo-particles. The last existing version of APMO
before it was merged into LOWDIN is capable of performing
HartreeFock (HF) and MP2 calculations for systems containing
any type and number of quantum species.[911]
On the other hand, PARAKATA implements Auxiliary Density
Functional Theory (ADFT),[12,13] Auxiliary Density Perturbation
Theory (ADPT)[14,15] and electron propagator theory (EPT) for
electronic structure.[1622] ADPT capabilities include calculation
of electronic contribution to static and dynamic dipole polarizabilities,[14] hyper-polarizabilities,[23] electronic and nuclear
Fukui function,[24,25] and other related fields such us the Shannons entropy response to molecular ionization.[26] As it is
inherent to, extensive use is made of auxiliary functions. Similarly to the deMon2k program,[27] auxiliary functions are generated automatically.[28,29] In contrast, PARAKATA uses Cartesian
auxiliary functions.[30] In addition, auxiliary functions can also
be used in HartreeFock and post-HartreeFock calculations,
such as in electron propagator calculations. In the latter, it has
been proven that only minor deviations are caused by using
auxiliary functions and the gain in efficiency is considerable.[31]
With the aim of extending the electronic structure methods
implemented in PARAKATA to study systems containing other
DOI: 10.1002/qua.24500
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computational challenges of the APMO theory and the LOWDIN code and strategies for the future.
Technical Details
LOWDIN has been designed to address two challenges:
It must be capable of performing calculations for systems
containing any type and number of quantum species.
It must have a clear programming standard to simplify
the implementation of new extensions.
In this context, LOWDIN has been fully coded in the FORTRAN 2003 standard, with some C/C11 bindings to external
libraries. Although FORTRAN 2003 is not a full Object Oriented
Programming (OOP) language, most OOP capabilities can be
easily emulated, such as class definitions, some polymorphism,
and inheritance.[32]
As observed in Figure 1, LOWDIN structure is based on a CORE
program with small programs around it. These programs are
completely encapsulated and independent from one another.
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2. Full convergence of electrons, if any, followed by one iteration for each nonelectronic species
3. One iteration for each quantum species until global convergence is achieved.
Convergence acceleration methods such as DIIS,[39] level
shifting,[40] and optimal damping[41] have been implemented
and are fully operational for any type of quantum species.
Capabilities
LOWDIN has been designed to be capable of handling different
representations of the wavefunctions of fermionic and bosonic
species. The current version of code supports Hartree-products,
Slater determinants, and symmetric permutations of spinorbitals. The SCF program can perform Hartree,[42] Hartree
Fock,[6] and DFT[43,44] calculations for any type of quantum
species.
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Figure 4. Left: Density contour (0.01 a.u.) of two Helium atoms confined in a fullerene. Right: HeAHe and HeAC60 potentials employed in the calculation.
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54
In our latest study, we have compared the electronic ionization potentials of isoelectronic muonic and all-electron atoms
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at the full-CI level.[52] We found that the differences in the ionization potentials are only of the order of meV. Furthermore,
we found that the difference in nuclear masses and the incomplete screening of the muon account for the observed discrepancies. Therefore, from these calculations we conclude that
muonelectron correlation as well as the muon relaxation
energy is negligible upon the removal of an electron. In addition, we quantified the partial muonic screening effect for the
H2 1 4Hel reaction[52] by comparing our calculated energy
barriers with those obtained considering infinite nuclear
masses H2 1 H. We observed that the partial muonic screening
reduces the energy barrier by 0.8 meV. Although this effect is
very small for most chemical applications, it should be considered for precise calculations aiming for spectroscopic accuracy.
We have calculated the APMO/EP2 positron binding energies of the 20 standard amino acids considering three different molecular conformations: classical,
H-bonded, and zwitterion (Charry et al., Chem. Phys. Lett. in
preparation). Our results are in good qualitative agreement with
those of Tachikawa and coworkers.[77] An analysis of these
results reveals that positron binding energies and densities vary
dramatically among the different conformers. Figure 7 depicts
APMO/HF positronic (in red) and electronic (in blue) densities of
a positronic glycine zwitterion. As observed in this figure, positron density is very delocalized throughout the molecule.
Positrons Chemistry.
Figure 7. APMO/HF electronic (in blue) and positronic (in red) density plots
for the positronic glycine zwitterion. A contour value of 0.001 was
employed.
Perspective
LOWDIN code stands out as a versatile platform for the efficient computational implementation of new theories and for
the quantum calculation of properties of regular and exotic
molecular systems. At the programming level, electronic structure modules are generalized to an APMO framework using
the OOP capabilities. From the theoretical and computational
perspectives, these extensions entail new challenges.
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[12] A. M. K
oster, J. U. Reveles, J. M. del Campo, J. Chem. Phys. 2004, 121,
3417.
[13] P. Calaminici, V. D. Domnguez-Soria, G. U. Flores-Moreno, R. GamboaMartnez, G. Geudtner, A. Goursot, D. R. Salahub, A. M. K
oster, In Handbook of Computational Chemistry, J. Leszczynski, Eds.; Springer: Netherlands, 2012, pp. 573610.
[14] R. Flores-Moreno, A. M. K
oster, J. Chem. Phys. 2008, 128, 134105.
[15] J. Carmona-Espndola, R. Flores-Moreno, A. M. K
oster, J. Chem. Phys.
2010, 133, 084102.
[21] Y. Ohrn,
G. Born, In Advances in Quantum Chemistry, Vol. 13; P.-O.
L
owdin, Eds.; Academic Press: New York, 1981; pp. 188.
[22] J. V. Ortiz, WIREs Comput. Mol. Sci. 2013, 03, 123.
[23] J. Carmona-Espndola, R. Flores-Moreno, A. M. K
oster, Int. J. Quantum
Chem. 2012, 112, 3461.
[24] R. Flores-Moreno, J. Melin, J. V. Ortiz, G. Merino, J. Chem. Phys. 2008,
129, 224105.
[25] R. Flores-Moreno, J. Chem. Theory Comput. 2010, 6, 48.
[26] K. Pineda-Urbina, R. D. Guerrero, A. Reyes, Z. G
omez-Sandoval, R.
Flores-Moreno, J. Mol. Mod. 2013, 19, 1677.
[27] A. M. K
oster, G. Geudtner, P. Calaminici, M.E. Casida, V.D. Dominguez, R.
Flores-Moreno, G.U. Gamboa, A. Goursot, T. Heine, A. Ipatov, F.
Janetzko, J. M. del Campo, J. U. Reveles, A. Vela, B. Zuniga-Gutierrez,
D.R. Salahub, demon2k, 2011, Available at: http://www.demon-software.com. Last accessed 2013/06/21.
[28] J. Andzelm, E. Radzio, D. R. Salahub, J. Comput. Chem. 1985, 6, 520.
[29] J. Andzelm, N. Russo, D. R. Salahub, J. Chem. Phys. 1987, 87, 6562.
[30] A. M. K
oster, J. Chem. Phys. 2003, 118, 9943.
[31] R. Flores-Moreno, J. V. Ortiz, J. Chem. Phys. 2009, 131, 124110.
[32] ISO/IEC 1539-1:2010, Information technology Programming languages Fortran Part 1: Base language; International Organization
for Standardization (ISO: Geneva), 2009.
[33] H. Nakai, Int. J. Quantum Chem. 2002, 86, 511.
[34] H. Nakai, M. Hoshino, K. Miyamoto, S. Hyodo, J. Chem. Phys. 2005, 122,
164101.
[35] F. Moncada, D. Cruz, A. Reyes, Chem. Phys. Lett. 2012, 539540, 209.
[36] S. Obara, A. Saika, J. Chem. Phys. 1986, 84, 3963.
[37] M. Head-Gordon, J. A. Pople, J. Chem. Phys. 1988, 89, 5777.
[38] J. T. Fermann, E. F. Valeev, Libint: Machine-generated library for efficient evaluation of molecular integrals over Gaussians, 2003, Available
at: http://sourceforge.net/p/libint. Last accessed 2013/06/21.
[39] P. Pulay, J. Comput. Chem. 1982, 3, 556.
[40] V. R. Saunders, I. H. Hillier, Int. J. Quantum Chem. 1973, 7, 699.
[41] E. Cance`s, C. Le Bris, Int. J. Quantum Chem. 2000, 79, 82.
[42] F. Moncada, S. Gonzalez, R. Flores-Moreno, A. Reyes, Mol. Phys.
(submitted).
[43] F. Moncada, E. Posada, R. Flores-Moreno, A. Reyes, Chem. Phys. 2012,
400, 103.
[44] J. Charry, F. Moncada, E. Posada, R. Flores-Moreno, A. Reyes, Chem.
Phys. (submitted).
[45] A. M. K
oster, J. U. Reveles, J. M. del Campo, J. Chem. Phys. 2004, 121,
3417.
[46] P. Dirac, Proc. R. Soc. London, Ser. A 1929, 123, 714.
56
[47]
[48]
[49]
[50]
[51]
[52]
[53]
[54]
[55]
[56]
[57]
[58]
[59]
[60]
[61]
[62]
[63]
[64]
[65]
[66]
[67]
[68]
[69]
[70]
[71]
[72]
[73]
[74]
[75]
[76]
[77]
[78]
[79]
[80]
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