P.W. Ayers

Fanpy: A Python Library for Prototyping Multideterminant Methods in Ab Initio Quantum Chemistry

T. D. Kim, M. Richer, G. Sánchez-Díaz, F. Heidar-Zadeh, T. Verstraelen, R.A. Miranda-Quintana, P.W. Ayers
physics.chem-ph
2021
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Abstract 

Fanpy is a free and open-source Python library for developing and testing multideterminant wavefunctions and related ab initio methods in electronic structure theory. The main use of Fanpy is to quickly prototype new methods by making it easier to transfer the mathematical conception of a new wavefunction ans¨atze to a working implementation. Fanpy uses the framework of our recently introduced Flexible Ansatz for N-electron Configuration Interaction (FANCI), where multideterminant wavefunctions are represented by their overlaps with Slater determinants of orthonormal spin-orbitals. In the simplest case, a new wavefunction ansatz can be implemented by simply writing a function for evaluating its overlap with an arbitrary Slater determinant. Fanpy is modular in both implementation and theory: the wavefunction model, the system’s Hamiltonian, and the choice of objective function are all independent modules. This modular structure makes it easy for users to mix and match different methods and for developers to quickly try new ideas. Fanpy is written purely in Python with standard dependencies, making it accessible for most operating systems; it adheres to principles of modern software development, including comprehensive documentation, extensive testing, and continuous integration and delivery protocols. This article is considered to be the official release notes for the Fanpy library.

Reactivity of Single Transition Metal Atoms on a Hydroxylated Amorphous Silica Surface: A Periodic Conceptual DFT Investigation

X. Deraet, J. Turek, M. Alonso, F. Tielens, S. Cottenier, P.W. Ayers, B.M. Weckhuysen, F. De Proft
Chemistry - A European Journal
27, 19 , 6050-6063
2021
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Abstract 

The drive to develop maximal atom-efficient catalysts coupled to the continuous striving for more sustainable reactions has led to an ever-increasing interest in single-atom catalysis. Based on a periodic conceptual density functional theory (cDFT) approach, fundamental insights into the reactivity and adsorption of single late transition metal atoms supported on a fully hydroxylated amorphous silica surface have been acquired. In particular, this investigation revealed that the influence of van der Waals dispersion forces is especially significant for a silver (98 %) or gold (78 %) atom, whereas the oxophilicity of the Group 8-10 transition metals plays a major role in the interaction strength of these atoms on the irreducible SiO2 support. The adsorption energies for the less-electronegative row 4 elements (Fe, Co, Ni) ranged from -1.40 to -1.92 eV, whereas for the heavier row 5 and 6 metals, with the exception of Pd, these values are between -2.20 and -2.92 eV. The deviating behavior of Pd can be attributed to a fully filled d-shell and, hence, the absence of the hybridization effects. Through a systematic analysis of cDFT descriptors determined by using three different theoretical schemes, the Fermi weighted density of states approach was identified as the most suitable for describing the reactivity of the studied systems. The main advantage of this scheme is the fact that it is not influenced by fictitious Coulomb interactions between successive, charged reciprocal cells. Moreover, the contribution of the energy levels to the reactivity is simultaneously scaled based on their position relative to the Fermi level. Finally, the obtained Fermi weighted density of states reactivity trends show a good agreement with the chemical characteristics of the investigated metal atoms as well as the experimental data.

IOData: A python library for reading, writing, and converting computational chemistry file formats and generating input files

T. Verstraelen, W. Adams, L. Pujal, A. Teherani, B. D. Kelly, L. Macaya, F. Meng, M. Richer, R. Hernández-Esparza, X. D. Yang, M. Chan, T. D. Kim, M. Cools-Ceuppens, V. Chuiko, E. Vohringer-Martinez, P.W. Ayers, F. Heidar-Zadeh
Journal of Computational Chemistry
45, 6, 458--464
2021
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Abstract 

IOData is a free and open‐source Python library for parsing, storing, and converting various file formats commonly used by quantum chemistry, molecular dynamics, and plane‐wave density‐functional‐theory software programs. In addition, IOData supports a flexible framework for generating input files for various software packages. While designed and released for stand‐alone use, its original purpose was to facilitate the interoperability of various modules in the HORTON and ChemTools software packages with external (third‐party) molecular quantum chemistry and solid‐state density‐functional‐theory packages. IOData is designed to be easy to use, maintain, and extend; this is why we wrote IOData in Python and adopted many principles of modern software development, including comprehensive documentation, extensive testing, continuous integration/delivery protocols, and package management. This article is the official release note of the IOData library.

Information-Theoretic Approaches to Atoms-in-Molecules: Hirshfeld Family of Partitioning Schemes

F. Heidar-Zadeh, P.W. Ayers, T. Verstraelen, I. Vinogradov, E. Vohringer-Martinez, P. Bultinck
Journal of Physical Chemistry A
112 (17) 4219-4245
2018
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Abstract 

Many population analysis methods are based on the precept that molecules should be built from fragments (typically atoms) that maximally resemble the isolated fragment. The resulting molecular building blocks are intuitive (because they maximally resemble well-understood systems) and transferable (because if two molecular fragments both resemble an isolated fragment, they necessarily resemble each other). Information theory is one way to measure the deviation between molecular fragments and their isolated counterparts, and it is a way that lends itself to interpretation. For example, one can analyze the relative importance of electron transfer and polarization of the fragments. We present key features, advantages, and disadvantages of the information-theoretic approach. We also codify existing information-theoretic partitioning methods in a way, that clarifies the enormous freedom one has within the information-theoretic ansatz.

Exploring the substrate selectivity of human sEH and M. tuberculosis EHB using QM/MM

S. Rabi, A.H.G. Patel, S.K. Burger, T. Verstraelen, P.W. Ayers
Structural Chemistry
28 (5), 1501-1511
2017
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Abstract 

The mechanisms of human soluble epoxide hydrolase (sEH) and the corresponding epoxide hydrolase enzyme from Mycobacterium tuberculosis (EHB) are studied computationally, using the quantum mechanics/molecular mechanics (QM/MM) method. To do this, we modeled the alkylation and the hydrolysis steps of three substrates: trans-1,3-diphenylpropene oxide, trans-stilbene oxide and cis-stilbene oxide. Studying the regioselectivity for trans-1,3-diphenylpropene oxide, we determined that both enzymes prefer ring opening via attack on the benzylic carbon. In agreement with experimental studies, our computations show that the rate-limiting step is hydrolysis of the ester intermediate, with reaction barriers of approximately 13 to 18 kcal/mol. Using the barrier energies of this rate-limiting step, the three epoxides were ranked in order of reactivity. Though the reactivity order was correctly predicted for sEH, the predicted order for EHB did not correspond to experimental observations. Next, the electrostatic contributions of individual residues on the barrier height of the rate-limiting step were also studied. This revealed several residues important for catalysis. The secondary tritium kinetic isotope effect for the alkylation step was determined using a cluster model for the active site of sEH. The calculated value was 1.27, suggesting a late transition state for the rate-limiting step. Finally, we analyzed the reactivity trends using reactivity indicators from conceptual density functional theory, allowing us to identify ease of electron transfer as the primary driving force for the reaction.

The local response of global descriptors

F. Heidar-Zadeh, S. Fias, E. Vohringer-Martinez, T. Verstraelen, P.W. Ayers
Theoretical Chemistry Accounts
136 (1), 19
2017
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Abstract 

We consider the problem of defining an appropriate local descriptor corresponding to an arbitrary global descriptor. Although it does not seem easy to rigorously and uniquely define local analogues of derived global descriptors (e.g., the electrophilicity) or the fundamental global descriptors associated with the canonical ensemble (e.g., the hardness), the local response of these global descriptors can be defined unambiguously. We look at the local response of the global electrophilicity and compare it to the conventional, ad hoc, definition of the local electrophilicity. The local response of global nucleofugality and electrofugality is also discussed.

Performance of Shannon-entropy compacted N-electron wave functions for configuration interaction methods

D.R. Alcoba, A. Torre, L. Lain, G. Massaccesi, O.B. Ona, P.W. Ayers, M. Van Raemdonck, P. Bultinck, D. Van Neck
Theoretical Chemistry Accounts
135 (6), 153
2016
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Abstract 

The coefficients of full configuration interaction wave functions (FCI) for N-electron systems expanded in N-electron Slater determinants depend on the orthonormal one-particle basis chosen although the total energy remains invariant. Some bases result in more compact wave functions, i.e. result in fewer determinants with significant expansion coefficients. In this work, the Shannon entropy, as a measure of information content, is evaluated for such wave functions to examine whether there is a relationship between the FCI Shannon entropy of a given basis and the performance of that basis in truncated CI approaches. The results obtained for a set of randomly picked bases are compared to those obtained using the traditional canonical molecular orbitals, natural orbitals, seniority minimising orbitals and a basis that derives from direct minimisation of the Shannon entropy. FCI calculations for selected atomic and molecular systems clearly reflect the influence of the chosen basis. However, it is found that there is no direct relationship between the entropy computed for each basis and truncated CI energies.

An Explicit Approach to Conceptual Density Functional Theory Descriptors of Arbitrary Order

F. Heidar-Zadeh, M. Richer, S. Fias, R.A. Miranda-Quintana, M. Chan, M. Franco-Perez, C. Gonzalez-Espinoza, T.D. Kim, C. Lanssens, A.H.G. Patel, X.D. Yang, E. Vohringer-Martinez, C. Cárdenas, T. Verstraelen, P.W. Ayers
Chemical Physics Letters
660, 307–312
2016
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Abstract 

We present explicit formulas for arbitrary-order derivatives of the energy, grand potential, electron density, and higher-order response functions with respect to the number of electrons, and the chemical potential for any smooth and differentiable model of the energy versus the number of electrons. The resulting expressions for global reactivity descriptors (hyperhardnesses and hypersoftnesses), local reactivity descriptors (hyperFukui functions and local hypersoftnesses), and nonlocal response functions are easy to evaluate computationally. Specifically, the explicit formulas for global/local/nonlocal hypersoftnesses of arbitrary order are derived using Bell polynomials. Explicit expressions for global and local hypersoftness indicators up to fifth order are presented.

When is the Fukui Function Not Normalized? The Danger of Inconsistent Energy Interpolation Models in Density Functional Theory

F. Heidar-Zadeh, R.A. Miranda-Quintana, T. Verstraelen, P. Bultinck, P.W. Ayers, A. Buekenhoudt
Journal of Chemical Theory and Computation (JCTC)
12 (12), 5777–5787
2016
A1

Abstract 

When one defines the energy of a molecule with a noninteger number of electrons by interpolation of the energy values for integer-charged states, the interpolated electron density, Fukui function, and higher-order derivatives of the density are generally not normalized correctly. The necessary and sufficient condition for consistent energy interpolation models is that the corresponding interpolated electron density is correctly normalized to the number of electrons. A necessary, but not sufficient, condition for correct normalization is that the energy interpolant be a linear function of the reference energies. Consistent with this general rule, polynomial interpolation models and, in particular, the quadratic E vs N model popularized by Parr and Pearson, do give normalized densities and density derivatives. Interestingly, an interpolation model based on the square root of the electron number also satisfies the normalization constraints. We also derive consistent least-norm interpolation models. In contrast to these models, the popular rational and exponential forms for E vs N do not give normalized electron densities and density derivatives.

Minimal Basis Iterative Stockholder: Atoms-in-Molecules for Force-Field Development

T. Verstraelen, S. Vandenbrande, F. Heidar-Zadeh, L. Vanduyfhuys, V. Van Speybroeck, M. Waroquier, P.W. Ayers
Journal of Chemical Theory and Computation (JCTC)
12(8), 3894-3912
2016
A1

Abstract 

Atomic partial charges appear in the Coulomb term of many force-field models and can be derived from electronic structure calculations with a myriad of atoms-in-molecules (AIM) methods. More advanced models have also been proposed, using the distributed nature of the electron cloud and atomic multipoles. In this work, an electrostatic force field is defined through a concise approximation of the electron density, for which the Coulomb interaction is trivially evaluated. This approximate "pro-density" is expanded in a minimal basis of atom-centered s-type Slater density functions, whose parameters are optimized by minimizing the Kullback-Leibler divergence of the pro-density from a reference electron density, e.g. obtained from an electronic structure calculation. The proposed method, Minimal Basis Iterative Stockholder (MBIS), is a variant of the Hirshfeld AIM method but it can also be used as a density-fitting technique. An iterative algorithm to refine the pro-density is easily implemented with a linear-scaling computational cost, enabling applications to supramolecular systems. The benefits of the MBIS method are demonstrated with systematic applications to molecular databases and extended models of condensed phases. A comparison to 14 other AIM methods shows its effectiveness when modeling electrostatic interactions. MBIS is also suitable for rescaling atomic polarizabilities in the Tkatchenko-Sheffler scheme for dispersion interactions.

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