P.W. Ayers

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
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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
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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.

CheMPS2: Improved DMRG-SCF routine and correlation functions

S. Wouters, W. Poelmans, S. De Baerdemacker, P.W. Ayers, D. Van Neck
Computer Physics Communications
191, 235-237
2015
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Abstract 

CheMPS2, our spin-adapted implementation of the density matrix renormalization group (DMRG) for ab initio quantum chemistry (Wouters et al., 2014), has several new features. A speed-up of the augmented Hessian Newton–Raphson DMRG self-consistent field (DMRG-SCF) routine is achieved with the direct inversion of the iterative subspace (DIIS). For extended molecules, the active space orbitals can be localized by maximizing the Edmiston–Ruedenberg cost function. These localized orbitals can be ordered according to the topology of the molecule by approximately minimizing the bandwidth of the exchange matrix with the Fiedler vector. The electronic structure can be analyzed by means of the two-orbital mutual information, spin, spin-flip, density, and singlet diradical correlation functions.

Non-Variational Orbital Optimization Techniques for the AP1roG Wave Function

K. Boguslawski, P. Tecmer, P.W. Ayers, P. Bultinck, S. De Baerdemacker, D. Van Neck
Journal of Chemical Theory and Computation (JCTC)
10 (11), 4873-4882
2014
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Abstract 

We introduce new nonvariational orbital optimization schemes for the antisymmetric product of one-reference orbital geminal (AP1roG) wave function (also known as pair-coupled cluster doubles) that are extensions to our recently proposed projected seniority-two (PS2-AP1roG) orbital optimization method [ J. Chem. Phys. 2014, 140, 214114)]. These approaches represent less stringent approximations to the PS2-AP1roG ansatz and prove to be more robust approximations to the variational orbital optimization scheme than PS2-AP1roG. The performance of the proposed orbital optimization techniques is illustrated for a number of well-known multireference problems: the insertion of Be into H2, the automerization process of cyclobutadiene, the stability of the monocyclic form of pyridyne, and the aromatic stability of benzene.

Efficient description of strongly correlated electrons with mean-field cost

K. Boguslawski, P. Tecmer, P.W. Ayers, P. Bultinck, S. De Baerdemacker, D. Van Neck
Physical Review B
89 (20), 201106
2014
A1

Abstract 

We present an efficient approach to the electron correlation problem that is well suited for strongly interacting many-body systems, but requires only mean-field-like computational cost. The performance of our approach is illustrated for one-dimensional Hubbard rings with different numbers of sites, and for the nonrelativistic quantum-chemical Hamiltonian exploring the symmetric dissociation of the H-50 hydrogen chain.

Open Access version available at UGent repository

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