P.W. Ayers

The Gradient Curves Method: An improved strategy for the derivation of molecular mechanics valence force fields from ab initio data

T. Verstraelen, D. Van Neck, P.W. Ayers, V. Van Speybroeck, M. Waroquier
LECTURE SERIES ON COMPUTER AND COMPUTATIONAL SCIENCES
Volume 7A-B, page 576 -+
2006
P1

Abstract 

A novel force-field parameterization procedure[1] is proposed that surmounts well-known difficulties of the conventional least squares parameterization. The multidimensional ab initio training data are first transformed into individual one-dimensional data sets, each associated with one term in the force-field model. In the second step conventional methods call be used to fit each energy term separately to its corresponding data set. The first step call be completed without any knowledge of the analytical expressions for the energy terms. Moreover the transformed data sets dictate the form of these expressions, which makes the method very suitable for deriving valence force fields. During the transformation in the first step, continuity and least-norm criteria are imposed. The latter facilitate the intuitive physical interpretation of the energy terms that are fitted to the transformed data sets, a prerequisite for transferable force fields. Benchmark parameterizations have been performed oil three small molecules, showing that the new method results in physically intuitive energy terms, exactly when a conventional parameterization would suffer from parameter correlations, i.e. when the number of redundant internal coordinates in the force-field model increases.

Constrained iterative Hirshfeld charges: A variational approach

L. Pujal, M. Van Zyl, E. Vohringer-Martinez, T. Verstraelen, P. Bultinck, P.W. Ayers, F. Heidar-Zadeh
Journal of Chemical Physics
Volume 156, Issue 19
2022
A1

Abstract 

We develop a variational procedure for the iterative Hirshfeld (HI) partitioning scheme. The main practical advantage of having a variational framework is that it provides a formal and straightforward approach for imposing constraints (e.g., fixed charges on certain atoms or molecular fragments) when computing HI atoms and their properties. Unlike many other variants of the Hirshfeld partitioning scheme, HI charges do not arise naturally from the information-theoretic framework, but only as a reverse-engineered construction of the objective function. However, the procedure we use is quite general and could be applied to other problems as well. We also prove that there is always at least one solution to the HI equations, but we could not prove that its self-consistent equations would always converge for any given initial pro-atom charges. Our numerical assessment of the constrained iterative Hirshfeld method shows that it satisfies many desirable traits of atoms in molecules and has the potential to surpass existing approaches for adding constraints when computing atomic properties.

Published under an exclusive license by AIP Publishing.

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
Journal of Computational Chemistry
44, 5, 697-709
2022
A1

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
A1

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. Tehrani, 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
A1

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
A1

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
A1

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
A1

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
A1

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
A1

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.

Pages

Subscribe to RSS - P.W. Ayers