Browsing by Author "Witek, Henryk A."

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Algorithm for generating generalized resonance structures of single zigzag chains based on interface theory
(2018-05-01)
Langner, Johanna
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Witek, Henryk A.
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應用化學系
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應用化學系分子科學碩博班
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Department of Applied Chemistry
An alternative formulation of the theory of generalized resonance structures (Clar covers) of single zigzag chains N(n), based on the novel concept of interfaces, is presented. The global structure of every Clar cover can be conveniently expressed as a unique sequence of n interfaces. The complete set of Clar covers is then robustly constructed as the complete set of walks of length on the associated interface connectivity graph. The presented algorithm is readily generalizable to an arbitrary class of benzenoid structures.
An Algorithm and FORTRAN Program for Automatic Computation of the Zhang-Zhang Polynomial of Benzenoids
(2012)
Chou, Chien-Pin
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Witek, Henryk A.
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應用化學系
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應用化學系分子科學碩博班
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Department of Applied Chemistry
"An automatic computer code is developed to calculate the Zhang-Zhang (ZZ) polynomial (aka Clar covering polynomial) for benzenoid systems. The code can be routinely applied to dense pericondensed benzenoids containing up to 500 carbon atoms. For catacondensed and quasi-linear pericondensed benzenoid systems, the limiting number of atoms is much larger and may exceed 10000. A parallel implementation of the code is also presented, which allows one to surpass these limits with a large number of CPUs. The developed program is applied for finding the ZZ polynomials of various classes of benzenoid systems; general techniques and algorithms applicable in this context are reviewed and discussed. A survey of new results obtained in that way is presented in a sequel to this paper [C.-P. Chou, Y. Li, and H.A. Witek, MATCH Commun. Math. Comput. Chem., submitted]."
Analytical Solutions of the Schrodinger Equation with Power Potentials
(2016-01-01)
Karwowski, Jacek
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Witek, Henryk A.
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應用化學系
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應用化學系分子科學碩博班
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Department of Applied Chemistry
Conditions for the existence of polynomial solutions of the Schrodinger equation with potentials which are linear combinations of powers of r ranging from -2 to 2m, where m is a non-negative integer, are derived and explicit expressions for the coefficients are given. Potentials with m = 0, 1, 2 are discussed in detail.
Analytical Solutions of the Schrodinger Equation with Power Potentials
(2016-01)
Karwowski, Jacek
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Witek, Henryk A.
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應用化學系
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應用化學系分子科學碩博班
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Department of Applied Chemistry
Conditions for the existence of polynomial solutions of the Schrodinger equation with potentials which are linear combinations of powers of r ranging from -2 to 2m, where m is a non-negative integer, are derived and explicit expressions for the coefficients are given. Potentials with m = 0, 1, 2 are discussed in detail.
Automatized Parameterization of DFTB Using Particle Swarm Optimization
(2016-01)
Chou, Chien-Pin
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Nishimura, Yoshifumi
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Fan, Chin-Chai
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Mazur, Grzegorz
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Irle, Stephan
We present a novel density-functional tight-binding (DFTB) parametrization toolkit developed to optimize the parameters of various DFTB models in a fully automatized fashion. The main features of the algorithm, based on the particle swarm optimization technique, are discussed, and a number of initial pilot applications of the developed methodology to molecular and solid systems are presented.
Automatized Parameterization of DFTB Using Particle Swarm Optimization
(2016-01-01)
Chou, Chien-Pin
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Nishimura, Yoshifumi
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Fan, Chin-Chai
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Mazur, Grzegorz
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Irle, Stephan
We present a novel density-functional tight-binding (DFTB) parametrization toolkit developed to optimize the parameters of various DFTB models in a fully automatized fashion. The main features of the algorithm, based on the particle swarm optimization technique, are discussed, and a number of initial pilot applications of the developed methodology to molecular and solid systems are presented.
Automatized Parameterization of the Density-functional Tight-binding Method. II. Two-center Integrals
(2016-01-01)
Witek, Henryk A.
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Chou, Chien-Pin
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Mazur, Grzegorz
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Nishimura, Yoshifumi
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Irle, Stephan
We present an efficient numerical integration scheme (TWOCENT) to be used in the context of automatized parameterization of the density-functional tight-binding (DFTB) method. The accuracy of the integration process is assessed and its range of applicability is discussed. The functionality of the developed code is tested by reproducing the electronic portion of the existing mio parameter sets and by reproducing a series of reference DFT band structures of elemental solids.
Automatized Parameterization of the Density-functional Tight-binding Method. II. Two-center Integrals
(2016-01)
Witek, Henryk A.
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Chou, Chien-Pin
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Mazur, Grzegorz
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Nishimura, Yoshifumi
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Irle, Stephan
We present an efficient numerical integration scheme (TWOCENT) to be used in the context of automatized parameterization of the density-functional tight-binding (DFTB) method. The accuracy of the integration process is assessed and its range of applicability is discussed. The functionality of the developed code is tested by reproducing the electronic portion of the existing mio parameter sets and by reproducing a series of reference DFT band structures of elemental solids.
Barrierless reactions between two closed-shell molecules. I. Dynamics of F(2)+CH(3)SCH(3) reaction
(2008-03-14)
Lu, Yu-Ju
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Lee, Lance
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Pan, Jun-Wei
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Xie, Tingxian
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Witek, Henryk A.
A detailed experimental and theoretical investigation of the first-reported barrierless reaction between two closed-shell molecules [J. Chem. Phys. 127, 101101 (2007)] is presented. The translational energy and angular distributions of two product channels, HF+CH(2)SFCH(3) and F+CH(3)SFCH(3), determined at several collision energies, have been analyzed to reveal the dynamics of the studied reaction. Detailed analysis of the experimental and computational results supports the proposed reaction mechanism involving a short-lived F-F-S(CH(3))(2) intermediate, which can be formed without any activation energy. Other possible reaction mechanisms have been discriminated. The decay of the intermediate and competition between the two product channels have been discussed. (c) 2008 American Institute of Physics.
Basis Set Convergence of the Post-CCSD(T) Contribution to Noncovalent Interaction Energies
(2014-08-01)
Smith, Daniel G. A.
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Jankowski, Piotr
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Slawik, Michal
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Witek, Henryk A.
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Patkowski, Konrad
We investigated the basis set convergence of high-order coupled-cluster interaction energy contributions for 21 small weakly bound complexes. By performing CCSDT(Q) calculations in at least the aug-cc-pVTZ basis set, and CCSDT calculations in at least aug-cc-pVQZ (aug-cc-pVTZ for one system), we found the convergence to be quite slow. In particular, the 6-31G*(0.25) and 6-31G**(0.25,0.15) bases advocated by Hobza et al. (J. Chem. Theory Comput. 2013, 9, 2151; ibid. 2013, 9, 3420) are unsuitable for the post-CCSD(T) effects, with average errors for the CCSDT(Q)-CCSD(T) interaction energy contribution of about 80% for 6-31G**(0.25,0.15) and 110% for 6-31G*(0.25). Upgrading the basis set to aug-cc-pVDZ reduces the average error to about 35% and extremely demanding CCSDT(Q)/aug-cc-pVTZ calculations are necessary for further improvement in accuracy. An error cancellation between basis set incompleteness effects at the CCSDT-CCSD(T) and CCSDT(Q)-CCSDT levels occurs for most (but not all) complexes, making it unproductive to carry out CCSDT calculations in a larger basis set than the more demanding CCSDT(Q) calculations. We also found that the frozen natural orbital approximation at the CCSDT and CCSDT(Q) levels works well only if the thresholds for discarding least occupied natural orbitals are very tight (significantly tighter than the thresholds recommended for molecular correlation energies in the original work of Rolik and Kallay, J. Chem. Phys. 2011, 134, 124111), making the performance gains quite limited. The interaction energy contributions through CCSDT(Q) are both a necessity and a bottleneck in the construction of top-accuracy interaction potentials and further improvements in the efficiency of high-order coupled-cluster calculations will be of great help.
Basis Set Convergence of the Post-CCSD(T) Contribution to Noncovalent Interaction Energies
(2014-08-01)
Smith, Daniel G. A.
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Jankowski, Piotr
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Slawik, Michal
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Witek, Henryk A.
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Patkowski, Konrad
We investigated the basis set convergence of high-order coupled-cluster interaction energy contributions for 21 small weakly bound complexes. By performing CCSDT(Q) calculations in at least the aug-cc-pVTZ basis set, and CCSDT calculations in at least aug-cc-pVQZ (aug-cc-pVTZ for one system), we found the convergence to be quite slow. In particular, the 6-31G*(0.25) and 6-31G**(0.25,0.15) bases advocated by Hobza et al. (J. Chem. Theory Comput. 2013, 9, 2151; ibid. 2013, 9, 3420) are unsuitable for the post-CCSD(T) effects, with average errors for the CCSDT(Q)-CCSD(T) interaction energy contribution of about 80% for 6-31G**(0.25,0.15) and 110% for 6-31G*(0.25). Upgrading the basis set to aug-cc-pVDZ reduces the average error to about 35% and extremely demanding CCSDT(Q)/aug-cc-pVTZ calculations are necessary for further improvement in accuracy. An error cancellation between basis set incompleteness effects at the CCSDT-CCSD(T) and CCSDT(Q)-CCSDT levels occurs for most (but not all) complexes, making it unproductive to carry out CCSDT calculations in a larger basis set than the more demanding CCSDT(Q) calculations. We also found that the frozen natural orbital approximation at the CCSDT and CCSDT(Q) levels works well only if the thresholds for discarding least occupied natural orbitals are very tight (significantly tighter than the thresholds recommended for molecular correlation energies in the original work of Rolik and Kallay, J. Chem. Phys. 2011, 134, 124111), making the performance gains quite limited. The interaction energy contributions through CCSDT(Q) are both a necessity and a bottleneck in the construction of top-accuracy interaction potentials and further improvements in the efficiency of high-order coupled-cluster calculations will be of great help.
Biconfluent Heun equation in quantum chemistry: Harmonium and related systems
(2014-05-11)
Karwowski, Jacek
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Witek, Henryk A.
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應用化學系
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應用化學系分子科學碩博班
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Department of Applied Chemistry
Schrodinger equation for harmonium and related models may be transformed to the biconfluent Heun equation. The solubility of this equation and its applications in quantum chemistry are briefly discussed.
Chemical clocks, oscillations, and other temporal effects in analytical chemistry: oddity or viable approach?
(2018-08-07)
Prabhu, Gurpur Rakesh D.
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Witek, Henryk A.
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Urban, Pawel L.
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交大名義發表
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應用化學系
Most analytical methods are based on analogue inputs from sensors of light, electric potentials, or currents. The signals obtained by such sensors are processed using certain calibration functions to determine concentrations of the target analytes. The signal readouts are normally done after an optimised and fixed time period, during which an assay mixture is incubated. This minireview covers anotherand somewhat unusualanalytical strategy, which relies on the measurement of time interval between the occurrences of two distinguishable states in the assay reaction. These states manifest themselves via abrupt changes in the properties of the assay mixture (e.g. change of colour, appearance or disappearance of luminescence, change in pH, variations in optical activity or mechanical properties). In some cases, a correlation between the time of appearance/disappearance of a given property and the analyte concentration can be also observed. An example of an assay based on time measurement is an oscillating reaction, in which the period of oscillations is linked to the concentration of the target analyte. A number of chemo-chronometric assays, relying on the existing (bio)transformations or artificially designed reactions, were disclosed in the past few years. They are very attractive from the fundamental point of view butso faronly few of them have be validated and used to address real-world problems. Then, can chemo-chronometric assays become a practical tool for chemical analysis? Is there a need for further development of such assays? We are aiming to answer these questions.
Choice of Optimal Shift Parameter for the Intruder State Removal Techniques in Multireference Perturbation Theory
(2012-11-01)
Chang, Shu-Wei
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Witek, Henryk A.
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應用化學系
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應用化學系分子科學碩博班
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Department of Applied Chemistry
An extensive critical evaluation of intruder state removal techniques (aka shift techniques) applicable to multireference perturbation theory (MRPT) shows that the magnitude of the shift parameter a does not influence the spectroscopic parameters of diatomics to a significant degree, provided that the shift is chosen to be sufficiently large. In such case, typical variation of spectroscopic parameters over a wide range of shift parameters is smaller than 0.005 angstrom for equilibrium distances, 30 cm(-1) for harmonic vibrational frequencies, and 0.1 eV for dissociation energies. It is found that large values of a not only remove intruder states but they also bring the MRPT energies and properties closer to experimental values. The presented analysis allows us to determine optimal values of the shift parameters to be used in conjunction with various versions of MRPT; these values are recommended to replace the ad hoc values of sigma suggested in MRPT manuals in calculations for diatomics. Transferability of the optimal shift parameters to larger molecular systems and to other basis sets than aug-cc-pVTZ is anticipated but remains to be formally established.
Choosing a proper complete active space in calculations for transition metal dimers: ground state of Mn(2) revisited
(2008)
Camacho, Cristopher
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Yamamoto, Shigeyoshi
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Witek, Henryk A.
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應用化學系分子科學碩博班
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Institute of Molecular science
The potential energy curve of the ground state of Mn(2) has been studied using a systematic sequence of complete active spaces. Deficiencies of the routinely used active space, built from atomic 4s and 3d orbitals, has been identified and discussed. It is shown that an additional sigma(g) orbital, originating from the atomic virtual 4p(z) orbitals, is essential for a proper description of static correlation in the 1 Sigma(+)(g) state of Mn(2). The calculated spectroscopic parameters of the 1 Sigma(+)(g) state agree well with available experimental data. The calculated equilibrium bond lengths are located between 3.24 and 3.50 angstrom, the harmonic vibrational frequencies, between 44 and 72 cm(-1), and the dissociation energies, between 0.05 and 0.09 eV. An urgent need for an accurate gas-phase experimental study of spectroscopic constants of Mn(2) is highlighted.
Closed-Form Formulas for the Zhang-Zhang Polynomials of Benzenoid Structures: Chevrons and Generalized Chevrons
(2014)
Chou, Chien-Pin
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Witek, Henryk A.
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應用化學系
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應用化學系分子科學碩博班
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Department of Applied Chemistry
Closed-form, general formulas for the Zhang-Zhang (ZZ) polynomials for two important classes of benzenoid structures, chevrons Ch(k, m, n) and generalized chevrons Ch(k, m, n(1), n(2)), are formally derived. The derivations rely on a new and important theorem, which states that the ZZ polynomial of two fused parallelograms can be represented as the product of the ZZ polynomials of the two separated fragments. This theoretical result seems to play an important role in the theory of pericondensed benzenoids and may prove useful for the process of discovering closed-form formulas of Zhang-Zhang polynomials of for a wide class of benzenoid structures.
Closed-form formulas for the Zhang-Zhang polynomials of benzenoid structures: Prolate rectangles and their generalizations
(2016-01-10)
Chou, Chien-Pin
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Kang, Jin-Su
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Witek, Henryk A.
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應用化學系
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應用化學系分子科學碩博班
We show that the Zhang-Zhang (ZZ) polynomial of a benzenoid obtained by fusing a parallelogram M(m, n) with an arbitrary benzenoid structure ABC can be simply computed as a product of the ZZ polynomials of both fragments. It seems possible to extend this important result also to cases where both fused structures are arbitrary Kekulean benzenoids. Formal proofs of explicit forms of the ZZ polynomials for prolate rectangles Pr(m, n) and generalized prolate rectangles Pr ([m(1), m(2), ..., m(n)], n) follow as a straightforward application of the general theory, giving ZZ (Pr (m, n), x) = (1 + (1 x) . m)(n) and ZZ(Pr([m(1), m(2), ..., m(n)), n), x) = Pi(n)(k=1)(1 + (1 + x) . m(k)). (C) 2015 Elsevier B.V. All rights reserved.
Comment on "Zhang-Zhang polynomials of cyclo-polyphenacenes" by Q. Guo, H. Deng, and D. Chen
(2012-05-01)
Chou, Chien-Pin
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Witek, Henryk A.
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應用化學系
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應用化學系分子科學碩博班
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Department of Applied Chemistry
Explicit formulas for computing the Zhang-Zhang polynomial of cyclo-polyphenacenes, presented by Guo et al. (J. Math. Chem. 46:347, 2009) are found to be erroneous. In the present comment, a corrected version of Theorem 4.2 is given. The new formulation has been extensively tested by comparison with the Zhang-Zhang polynomials computed by brute force using a new, completely automatized computer code.
COMP 105-Prediction of Raman spectra in novel polyyne@SWNT peapods using dispersion-augmented density-functional-tight-binding
(2007-08-19)
Irle, Stephan
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Witek, Henryk A.
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Shinohara, Hisanori
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Morokuma, Keiji
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應用化學系
Comparison of Geometric, Electronic, and Vibrational Properties for All Pentagon/Hexagon-Bearing Isomers of Fullerenes C(38), C(40), and C(42)
(2009-08-05)
Malolepsza, Edyta
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Lee, Yuan-Pern
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Witek, Henryk A.
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Irle, Stephan
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Lin, Chun-Fu
The self-consistent-charge density-functional tight-binding (SCC-DFTB) method is employed for computing geometric, electronic, and vibrational properties for various topological isomers of small fullerenes. We consider all pentagon/hexagon-bearing isomers of C(38), C(40), and C(42) as the second part of a larger effort to catalogue the CC distance distributions, valence CCC angle distributions, electronic densities of states (DOSs), vibrational densities of states (VDOSs), and infrared (IR) and Raman spectra for fullerenes C(20)-C(180) [analogous data for C(20)-C(36) were published previously in Malolepsza et al., J Phys Chem A, 2007, 111, 6649]. Common features among the fullerenes are identified and properties characteristic for each specific fullerene cage size are discussed. (c) 2009 Wiley Periodicals, Inc. Int J Quantum Chem 109: 1999-2011, 2009