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Livraghi M, Pahi S, Nowakowski P, Smith DM, Wick CR, Smith AS. Block Chemistry for Accurate Modeling of Epoxy Resins. J Phys Chem B 2023; 127:7648-7662. [PMID: 37616478 PMCID: PMC10493980 DOI: 10.1021/acs.jpcb.3c04724] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 07/26/2023] [Indexed: 08/26/2023]
Abstract
Accurate molecular modeling of the physical and chemical behavior of highly cross-linked epoxy resins at the atomistic scale is important for the design of new property-optimized materials. However, a systematic approach to parametrizing and characterizing these systems in molecular dynamics is missing. We therefore present a unified scheme to derive atomic charges for amine-based epoxy resins, in agreement with the AMBER force field, based on defining reactive fragments─blocks─building the network. The approach is applicable to all stages of curing from pure liquid to gelation to fully cured glass. We utilize this approach to study DGEBA/DDS epoxy systems, incorporating dynamic topology changes into atomistic molecular dynamics simulations of the curing reaction with 127,000 atoms. We study size effects in our simulations and predict the gel point utilizing a rigorous percolation theory to recover accurately the experimental data. Furthermore, we observe excellent agreement between the estimated and the experimentally determined glass transition temperatures as a function of curing rate. Finally, we demonstrate the quality of our model by the prediction of the elastic modulus based on uniaxial tensile tests. The presented scheme paves the way for a broadly consistent approach for modeling and characterizing all amine-based epoxy resins.
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Affiliation(s)
- Mattia Livraghi
- Friedrich-Alexander-Universität
Erlangen-Nürnberg (FAU), Institute for Theoretical Physics,
PULS Group, Interdisciplinary Center for Nanostructured Films (IZNF), Cauerstrasse 3, Erlangen 91058, Germany
| | - Sampanna Pahi
- Friedrich-Alexander-Universität
Erlangen-Nürnberg (FAU), Institute for Theoretical Physics,
PULS Group, Interdisciplinary Center for Nanostructured Films (IZNF), Cauerstrasse 3, Erlangen 91058, Germany
| | - Piotr Nowakowski
- Group
for Computational Life Sciences, Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, Zagreb 10000, Croatia
| | - David M. Smith
- Group
for Computational Life Sciences, Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, Zagreb 10000, Croatia
| | - Christian R. Wick
- Friedrich-Alexander-Universität
Erlangen-Nürnberg (FAU), Institute for Theoretical Physics,
PULS Group, Interdisciplinary Center for Nanostructured Films (IZNF), Cauerstrasse 3, Erlangen 91058, Germany
| | - Ana-Sunčana Smith
- Friedrich-Alexander-Universität
Erlangen-Nürnberg (FAU), Institute for Theoretical Physics,
PULS Group, Interdisciplinary Center for Nanostructured Films (IZNF), Cauerstrasse 3, Erlangen 91058, Germany
- Group
for Computational Life Sciences, Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, Zagreb 10000, Croatia
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Jensen F. Unifying Charge-Flow Polarization Models. J Chem Theory Comput 2023. [PMID: 37365806 DOI: 10.1021/acs.jctc.3c00341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
We show that several models where electric polarization in molecular systems is modeled by charge-flow between atoms can all be considered as different manifestations of a general underlying mathematical structure. The models can be classified according to whether they employ atomic or bond parameters and whether they employ atom/bond hardness or softness. We show that an ab initio calculated charge response kernel can be considered as the inverse screened Coulombic matrix projected onto the zero-charge subspace, and this may provide a method for deriving charge screening functions to be used in force fields. The analysis suggests that some models contain redundancies, and we argue that a parameterization of charge-flow models in terms of bond softness is preferable as it depends on local quantities and decay to zero upon bond dissociation, while bond hardness depends on global quantities and increases toward infinity upon bond dissociation.
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Affiliation(s)
- Frank Jensen
- Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus DK-8000, Denmark
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3
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Choi S, Park A, Seo D, Lee WB, Nam KM, Kim Y, Chang J. Redox-Transition from Irreversible to Reversible Vitamin C by Pore Confinement in Microporous Carbon Network. ACS APPLIED MATERIALS & INTERFACES 2022; 14:36557-36569. [PMID: 35917313 DOI: 10.1021/acsami.2c07719] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Enhancement of redox-reversibility in electroactive species has been studied because of fundamental interest and their importance for energy storage systems. Various electroactive molecules suffer from redox-irreversible behavior, and this is a critical reason for their exclusion as redox electrolytes in energy storage systems. In this article, we fully demonstrated that ascorbic acid (ASC), which is an abundant but redox-irreversible molecule, can become redox-reversible when it is confined in microporous carbon regimes. From a theoretical perspective, redox-reversibility in an electrochemical reaction coupled with an irreversible chemical process can be greatly enhanced due to kinetic acceleration toward the inverse direction of the chemical reaction by accumulation of products in the nanoconfined regime. However, the kinetic acceleration in a nanoconfined domain shows limitations for enhancing the redox-reversibility, which indicates that stabilization of the species undergoing an irreversible chemical process is another important factor for redox-reversibility enhancement. The origin of nanoporous confinement of ASC and its enhanced redox-reversibility was rationalized by molecular dynamics simulations. We found that ASC-clusters of a fully protonated ASC and its conjugated base formed inside carbon pores, which would be a main driving force for its confinement in microporous carbon networks. Lastly, we demonstrated a prototype energy storage device using redox-reversible ASC in microporous carbon as the half electrode, which shows the feasibility of ASC as a possible redox electrolyte in an aqueous energy storage system.
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Affiliation(s)
- Sarah Choi
- Department of Chemistry and Research Institute for Convergence of Basic Science, Hanyang University, Seoul 04763, Republic of Korea
| | - Anseong Park
- Department of Chemical and Biological Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Dongho Seo
- Department of Chemistry and Chemistry Institute of Functional Materials, Pusan National University, Busan 46241, Republic of Korea
| | - Won Bo Lee
- Department of Chemical and Biological Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Ki Min Nam
- Department of Chemistry and Chemistry Institute of Functional Materials, Pusan National University, Busan 46241, Republic of Korea
| | - YongJoo Kim
- School of Advanced Materials Engineering, Kookmin University, Seoul 02707, Republic of Korea
| | - Jinho Chang
- Department of Chemistry and Research Institute for Convergence of Basic Science, Hanyang University, Seoul 04763, Republic of Korea
- Department of HY-KIST Bio-convergence, Hanyang University, Seoul 04763, Republic of Korea
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Gergs T, Schmidt F, Mussenbrock T, Trieschmann J. Generalized Method for Charge-Transfer Equilibration in Reactive Molecular Dynamics. J Chem Theory Comput 2021; 17:6691-6704. [PMID: 34672567 DOI: 10.1021/acs.jctc.1c00382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Variable charge models (e.g., electronegativity equalization method (EEM), charge equilibration (QEq), electrostatic plus (ES+)) used in reactive molecular dynamics simulations often inherently impose a global charge transfer between atoms (approximating each system as an ideal metal). Consequently, most surface processes (e.g., adsorption, desorption, deposition, sputtering) are affected, potentially causing dubious dynamics. This issue has been addressed by certain split charge variants (i.e., split charge equilibration (SQE), redoxSQE) through a distance-dependent bond hardness, by the atomic charge ACKS2 and QTPIE models, which are based on the Kohn-Sham density functional theory, as well as by an electronegativity screening extension to the QEq model (approximating each system as an ideal insulator). In a brief review of the QEq and the QTPIE model, their applicability for studying surface interactions is assessed in this work. Following this evaluation, a revised generalization of the QEq and QTPIE models is proposed and formulated, called the charge-transfer equilibration model or in short the QTE model. This method is based on the equilibration of charge-transfer variables, which locally constrain the split charge transfer per unit time (i.e., due to overlapping orbitals) without any kind of bond hardness specification. Furthermore, a formalism relying solely on atomic charges is obtained by a respective transformation, employing an extended Lagrangian method. We moreover propose a mirror boundary condition and its implementation to accelerate surface investigations. The models proposed in this work facilitate reactive molecular dynamics simulations, which describe various materials and surface phenomena appropriately.
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Affiliation(s)
- Tobias Gergs
- Chair of Applied Electrodynamics and Plasma Technology, Department of Electrical Engineering and Information Science, Ruhr University Bochum, 44801 Bochum, Germany.,Electrodynamics and Physical Electronics Group, Brandenburg University of Technology Cottbus-Senftenberg, Siemens-Halske-Ring 14, 03046 Cottbus, Germany
| | - Frederik Schmidt
- Chair of Applied Electrodynamics and Plasma Technology, Department of Electrical Engineering and Information Science, Ruhr University Bochum, 44801 Bochum, Germany
| | - Thomas Mussenbrock
- Chair of Applied Electrodynamics and Plasma Technology, Department of Electrical Engineering and Information Science, Ruhr University Bochum, 44801 Bochum, Germany
| | - Jan Trieschmann
- Electrodynamics and Physical Electronics Group, Brandenburg University of Technology Cottbus-Senftenberg, Siemens-Halske-Ring 14, 03046 Cottbus, Germany
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AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules. J Cheminform 2015; 7:50. [PMID: 26500704 PMCID: PMC4613891 DOI: 10.1186/s13321-015-0099-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 10/08/2015] [Indexed: 01/24/2023] Open
Abstract
Background Partial atomic charges are a well-established concept, useful in understanding and modeling the chemical behavior of molecules, from simple compounds, to large biomolecular complexes with many reactive sites. Results This paper introduces AtomicChargeCalculator (ACC), a web-based application for the calculation and analysis of atomic charges which respond to changes in molecular conformation and chemical environment. ACC relies on an empirical
method to rapidly compute atomic charges with accuracy comparable to quantum mechanical approaches. Due to its efficient implementation, ACC can handle any type of molecular system, regardless of size and chemical complexity, from drug-like molecules to biomacromolecular complexes with hundreds of thousands of atoms. ACC writes out atomic charges into common molecular structure files, and offers interactive facilities for statistical analysis and comparison of the results, in both tabular and graphical form. Conclusions Due to high customizability and speed, easy streamlining and the unified platform for calculation and analysis, ACC caters to all fields of life sciences, from drug design to nanocarriers. ACC is freely available via the Internet at http://ncbr.muni.cz/ACC. Electronic supplementary material The online version of this article (doi:10.1186/s13321-015-0099-x) contains supplementary material, which is available to authorized users.
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Verstraelen T, Vandenbrande S, Ayers PW. Direct computation of parameters for accurate polarizable force fields. J Chem Phys 2015; 141:194114. [PMID: 25416881 DOI: 10.1063/1.4901513] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
We present an improved electronic linear response model to incorporate polarization and charge-transfer effects in polarizable force fields. This model is a generalization of the Atom-Condensed Kohn-Sham Density Functional Theory (DFT), approximated to second order (ACKS2): it can now be defined with any underlying variational theory (next to KS-DFT) and it can include atomic multipoles and off-center basis functions. Parameters in this model are computed efficiently as expectation values of an electronic wavefunction, obviating the need for their calibration, regularization, and manual tuning. In the limit of a complete density and potential basis set in the ACKS2 model, the linear response properties of the underlying theory for a given molecular geometry are reproduced exactly. A numerical validation with a test set of 110 molecules shows that very accurate models can already be obtained with fluctuating charges and dipoles. These features greatly facilitate the development of polarizable force fields.
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Affiliation(s)
- Toon Verstraelen
- Center for Molecular Modeling (CMM), Member of the QCMM Ghent-Brussels Alliance, Ghent University, Technologiepark 903, B9000 Ghent, Belgium
| | - Steven Vandenbrande
- Center for Molecular Modeling (CMM), Member of the QCMM Ghent-Brussels Alliance, Ghent University, Technologiepark 903, B9000 Ghent, Belgium
| | - Paul W Ayers
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
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8
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Verstraelen T, Bultinck P. Can the electronegativity equalization method predict spectroscopic properties? SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 136 Pt A:76-80. [PMID: 24290357 DOI: 10.1016/j.saa.2013.10.124] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 10/25/2013] [Accepted: 10/31/2013] [Indexed: 06/02/2023]
Abstract
The electronegativity equalization method is classically used as a method allowing the fast generation of atomic charges using a set of calibrated parameters and provided knowledge of the molecular structure. Recently, it has started being used for the calculation of other reactivity descriptors and for the development of polarizable and reactive force fields. For such applications, it is of interest to know whether the method, through the inclusion of the molecular geometry in the Taylor expansion of the energy, would also allow sufficiently accurate predictions of spectroscopic data. In this work, relevant quantities for IR spectroscopy are considered, namely the dipole derivatives and the Cartesian Hessian. Despite careful calibration of parameters for this specific task, it is shown that the current models yield insufficiently accurate results.
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Affiliation(s)
- T Verstraelen
- Center for Molecular Modeling (CMM), Ghent University, 9000 Gent, Belgium.
| | - P Bultinck
- Ghent University, Department of Inorganic and Physical Chemistry, Krijgslaan 281 (S3), 9000 Gent, Belgium
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Affiliation(s)
- Chunyu Li
- Department of Materials Engineering and Birck Nanotechnology Center, Purdue University; West Lafayette Indiana 47906
| | - Alejandro Strachan
- Department of Materials Engineering and Birck Nanotechnology Center, Purdue University; West Lafayette Indiana 47906
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10
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Cavalcante ADO, Ribeiro MCC, Skaf MS. Polarizability effects on the structure and dynamics of ionic liquids. J Chem Phys 2014; 140:144108. [DOI: 10.1063/1.4869143] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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11
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Leven I, Azuri I, Kronik L, Hod O. Inter-layer potential for hexagonal boron nitride. J Chem Phys 2014; 140:104106. [DOI: 10.1063/1.4867272] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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12
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Comba P, Martin B, Sanyal A. An efficient fluctuating charge model for transition metal complexes. J Comput Chem 2013; 34:1598-608. [DOI: 10.1002/jcc.23297] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 03/18/2013] [Accepted: 03/22/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Peter Comba
- Anorganisch-Chemisches Institut; Universität Heidelberg; INF 270; D-69120; Heidelberg; Germany
| | - Bodo Martin
- Anorganisch-Chemisches Institut; Universität Heidelberg; INF 270; D-69120; Heidelberg; Germany
| | - Avik Sanyal
- Anorganisch-Chemisches Institut; Universität Heidelberg; INF 270; D-69120; Heidelberg; Germany
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13
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Verstraelen T, Ayers PW, Van Speybroeck V, Waroquier M. ACKS2: Atom-condensed Kohn-Sham DFT approximated to second order. J Chem Phys 2013; 138:074108. [DOI: 10.1063/1.4791569] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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14
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Tongyan P, Yang L, Zhaoyang W. Development of an atomistic-based chemophysical environment for modelling asphalt oxidation. Polym Degrad Stab 2012. [DOI: 10.1016/j.polymdegradstab.2012.07.032] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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15
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Pan T, Sun L, Yu Q. An atomistic-based chemophysical environment for evaluating asphalt oxidation and antioxidants. J Mol Model 2012; 18:5113-26. [PMID: 22772829 DOI: 10.1007/s00894-012-1512-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Accepted: 06/15/2012] [Indexed: 11/24/2022]
Abstract
Asphalt binders in service conditions are subject to oxidative aging that involves the reactions between oxygen molecules and the component species of bulk asphalt. As a result, significant alterations can occur to the desired physical and/or mechanical properties of asphalt. A common practice to alleviate asphalt aging has been to employ different chemical additives or modifiers as antioxidants. The current state of knowledge in asphalt oxidation and antioxidant evaluation is centered on determining the degradation of asphalt physical properties, mainly the viscosity and ductility. Such practices, although meeting direct engineering needs, do not contribute to the fundamental understanding of the aging and anti-oxidation mechanisms, and thereby developing anti-aging strategies. From this standpoint, this study was initiated to study the chemical and physical bases of asphalt oxidation, as well as the anti-oxidation mechanisms of bio-based antioxidants using the coniferyl-alcohol lignin as an example. A quantum chemistry (QC) based chemophysical environment is developed, in which the various chemical reactions between asphalt component species and oxygen, as well as the incurred physical changes are studied. X-ray photoelectron spectroscopy (XPS) was used to validate the modified and unmodified asphalt models.
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Affiliation(s)
- Tongyan Pan
- The Catholic University of America, Washington, DC 20064, USA.
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16
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Pan T, Lu Y, Lloyd S. Quantum-Chemistry Study of Asphalt Oxidative Aging: An XPS-Aided Analysis. Ind Eng Chem Res 2012. [DOI: 10.1021/ie3007215] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tongyan Pan
- The Catholic University, 620 Michigan Avenue, N.E., Washington, DC 20064, United States
| | - Yang Lu
- Institute for Research in Electronics
and Applied Physics, Energy Research Building, No. 223, University of Maryland, College Park, Maryland 20742-3511,
United States
| | - Stephen Lloyd
- The Catholic University, 620 Michigan Avenue, N.E., Washington, DC 20064, United States
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Pan T, van Duin ACT. Steel Surface Passivation at a Typical Ambient Condition: Atomistic Modeling and X-ray Diffraction/Reflectivity Analyses. Electrocatalysis (N Y) 2011. [DOI: 10.1007/s12678-011-0068-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Pan T. Quantum chemistry-based study of iron oxidation at the iron–water interface: An X-ray analysis aided study. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.06.041] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Verstraelen T, Bultinck P, Van Speybroeck V, Ayers PW, Van Neck D, Waroquier M. The Significance of Parameters in Charge Equilibration Models. J Chem Theory Comput 2011; 7:1750-64. [DOI: 10.1021/ct200006e] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- T. Verstraelen
- Center for Molecular Modeling, QCMM Alliance Ghent-Brussels, Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium
| | - P. Bultinck
- Department of Inorganic and Physical Chemistry, QCMM Alliance Ghent-Brussels, Ghent University, Krijgslaan 281 (S-3), B-9000 Gent, Belgium
| | - V. Van Speybroeck
- Center for Molecular Modeling, QCMM Alliance Ghent-Brussels, Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium
| | - P. W. Ayers
- Department of Chemistry, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada
| | - D. Van Neck
- Center for Molecular Modeling, QCMM Alliance Ghent-Brussels, Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium
| | - M. Waroquier
- Center for Molecular Modeling, QCMM Alliance Ghent-Brussels, Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium
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Puranen JS, Vainio MJ, Johnson MS. Accurate conformation-dependent molecular electrostatic potentials for high-throughput in silico drug discovery. J Comput Chem 2010; 31:1722-32. [PMID: 20020481 DOI: 10.1002/jcc.21460] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The atom-centered partial charges-approximation is commonly used in current molecular modeling tools as a computationally inexpensive alternative to quantum mechanics for modeling electrostatics. Even today, the use of partial charges remains useful despite significant advances in improving the efficiency of ab initio methods. Here, we report on new parameters for the EEM and SFKEEM electronegativity equalization-based methods for rapidly determining partial charges that will accurately model the electrostatic potential of flexible molecules. The developed parameters cover most pharmaceutically relevant chemistries, and charges obtained using these parameters reproduce the B3LYP/cc-pVTZ reference electrostatic potential of a set of FDA-approved drug molecules at best to an average accuracy of 13 +/- 4 kJ mol(-1); thus, equipped with these parameters electronegativity equalization-based methods rival the current best non-quantum mechanical methods, such as AM1-BCC, in accuracy, yet incur a lower computational cost. Software implementations of EEM and SFKEEM, including the developed parameters, are included in the conformer-generation tool BALLOON, available free of charge at http://web.abo.fi/fak/mnf/bkf/research/johnson/software.php.
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Affiliation(s)
- J Santeri Puranen
- Structural Bioinformatics Laboratory, Department of Biochemistry and Pharmacy, Abo Akademi University, Tykistökatu 6A (BioCity), FI-20520 Turku, Finland.
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Verstraelen T, Van Speybroeck V, Waroquier M. The electronegativity equalization method and the split charge equilibration applied to organic systems: Parametrization, validation, and comparison. J Chem Phys 2009; 131:044127. [DOI: 10.1063/1.3187034] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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23
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Zhang M, Fournier R. Self-consistent charge equilibration method and its application to Au13Na(n) (n = 1,10) clusters. J Phys Chem A 2009; 113:3162-70. [PMID: 19320517 DOI: 10.1021/jp8063273] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We modified the charge equilibration method (QEq) of Rappe et al. by including the third and fourth order terms in the series expansion for the energy of charged atoms. This leads to a self-consistent scheme for obtaining charges and total energy in a molecule. We combined the modified QEq with a scaled morse potential (SMP) to get a new potential, SMP/QEq. The SMP/QEq method allows to do realistic geometry optimizations and calculate reliable charge distributions and ionization energies. The performance of SMP/QEq was fully tested by comparing to high level theories and experiments. We established a connection between first-principles DFT and SMP/QEq which gives insight into SMP/QEq and suggests ways to improve it.
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Affiliation(s)
- Min Zhang
- Department of Physics & Astronomy, York University, Toronto, Ontario, Canada M3J 1P3
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Ouyang Y, Ye F, Liang Y. A modified electronegativity equalization method for fast and accurate calculation of atomic charges in large biological molecules. Phys Chem Chem Phys 2009; 11:6082-9. [DOI: 10.1039/b821696g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Mathieu D. Split charge equilibration method with correct dissociation limits. J Chem Phys 2007; 127:224103. [DOI: 10.1063/1.2803060] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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26
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Berente I, Czinki E, Náray-Szabó G. A combined electronegativity equalization and electrostatic potential fit method for the determination of atomic point charges. J Comput Chem 2007; 28:1936-42. [PMID: 17450564 DOI: 10.1002/jcc.20676] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We report an approach for the determination of atomic monopoles of macromolecular systems using connectivity and geometry parameters alone. The method is appropriate also for the calculation of charge distributions based on the quantum mechanically determined wave function and does not suffer from the mathematical instability of other electrostatic potential fit methods.
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Affiliation(s)
- Imre Berente
- Institute of Chemistry, Eötvös Loránd University, Pázmány Péter St. 1A, H-1117 Budapest, Hungary.
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Vareková RS, Koca J. Optimized and parallelized implementation of the electronegativity equalization method and the atom-bond electronegativity equalization method. J Comput Chem 2006; 27:396-405. [PMID: 16381078 DOI: 10.1002/jcc.20344] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The most common way to calculate charge distribution in a molecule is ab initio quantum mechanics (QM). Some faster alternatives to QM have also been developed, the so-called "equalization methods" EEM and ABEEM, which are based on DFT. We have implemented and optimized the EEM and ABEEM methods and created the EEM SOLVER and ABEEM SOLVER programs. It has been found that the most time-consuming part of equalization methods is the reduction of the matrix belonging to the equation system generated by the method. Therefore, for both methods this part was replaced by the parallel algorithm WIRS and implemented within the PVM environment. The parallelized versions of the programs EEM SOLVER and ABEEM SOLVER showed promising results, especially on a single computer with several processors (compact PVM). The implemented programs are available through the Web page http://ncbr.chemi.muni.cz/~n19n/eem_abeem.
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Affiliation(s)
- R Svobodová Vareková
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlárská 2, 611 37 Brno, Czech Republic
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Atomic Charges via Electronegativity Equalization: Generalizations and Perspectives. ADVANCES IN QUANTUM CHEMISTRY 2006. [DOI: 10.1016/s0065-3276(06)51004-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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29
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Dipole moments of water molecules confined in Na–LSX zeolites – Molecular dynamics simulations including polarization of water. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2005.09.130] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Bultinck P, Vanholme R, Popelier PLA, De Proft F, Geerlings P. High-Speed Calculation of AIM Charges through the Electronegativity Equalization Method. J Phys Chem A 2004. [DOI: 10.1021/jp046928l] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- P. Bultinck
- Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S-3), B-9000 Gent, Belgium, School of Chemistry, University of Manchester, Manchester M60 1QD, Great Britain, and Eenheid Algemene Chemie (ALGC), Free University of Brussels (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
| | - R. Vanholme
- Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S-3), B-9000 Gent, Belgium, School of Chemistry, University of Manchester, Manchester M60 1QD, Great Britain, and Eenheid Algemene Chemie (ALGC), Free University of Brussels (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
| | - P. L. A. Popelier
- Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S-3), B-9000 Gent, Belgium, School of Chemistry, University of Manchester, Manchester M60 1QD, Great Britain, and Eenheid Algemene Chemie (ALGC), Free University of Brussels (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
| | - F. De Proft
- Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S-3), B-9000 Gent, Belgium, School of Chemistry, University of Manchester, Manchester M60 1QD, Great Britain, and Eenheid Algemene Chemie (ALGC), Free University of Brussels (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
| | - P. Geerlings
- Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S-3), B-9000 Gent, Belgium, School of Chemistry, University of Manchester, Manchester M60 1QD, Great Britain, and Eenheid Algemene Chemie (ALGC), Free University of Brussels (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
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31
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Smirnov K, Bougeard D. Including the polarization in simulations of hydrated aluminosilicates. Model and application to water in silicalite. Chem Phys 2003. [DOI: 10.1016/s0301-0104(03)00275-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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34
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Sefcik J, Demiralp E, Cagin T, Goddard WA. Dynamic Charge Equilibration-Morse stretch force field: application to energetics of pure silica zeolites. J Comput Chem 2002; 23:1507-14. [PMID: 12395420 DOI: 10.1002/jcc.10130] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We present the Dynamic Charge Equilibration (DQEq) method for a self-consistent treatment of charge transfer in force field modeling, where atomic charges are designed to reproduce electrostatic potentials calculated quantum mechanically. Force fields coupled with DQEq allow charges to readjust as geometry changes in classical simulations, using appropriate algorithms for periodic boundary conditions. The full electrostatic energy functional is used to derive the corresponding forces and the second derivatives (hessian) for vibrational calculations. Using DQEq electrostatics, we develop a simple nonbond force field for simulation of silica molecular sieves, where nonelectrostatic interactions are described by two-body Morse stretch terms. Energy minimization calculations with the new force field yield accurate unit cell geometries for siliceous zeolites. Relative enthalpies with respect to quartz and third-law entropies calculated from harmonic vibrational analysis agree very well with available calorimetric data: calculated SiO(2) enthalpies relative to alpha-quartz are within 2 kJ/mol and entropies at 298 K are within 3 J/mol K of the respective experimental values. Contributions from the zero point energy and vibrational degrees of freedom were found to be only about 1 kJ/mol for the free energy of mutual transformations between microporous silica polymorphs. The approach presented here can be applied to interfaces and other oxides as well and it is suitable for development of force fields for accurate modeling of geometry and energetics of microporous and mesoporous materials, while providing a realistic description of electrostatic fields near surfaces and inside pores of adsorbents and catalysts.
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Affiliation(s)
- Jan Sefcik
- Swiss Federal Institute of Technology Zurich, Laboratorium für Technische Chemie, ETH Hönggerberg/HCI, CH-8093 Zürich, Switzerland
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35
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Bultinck P, Langenaeker W, Lahorte P, De Proft F, Geerlings P, Van Alsenoy C, Tollenaere JP. The Electronegativity Equalization Method II: Applicability of Different Atomic Charge Schemes. J Phys Chem A 2002. [DOI: 10.1021/jp020547v] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- P. Bultinck
- Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S-3), B-9000 Gent, Belgium, Molecular Design and Chemoinformatics, Johnson & Johnson Pharmaceutical Research and Development, Turnhoutseweg 30, B-2340 Beerse, Belgium, European Patent Office, Bayerstrasse 34, D-80335 Munich, Germany, Eenheid Algemene Chemie (ALGC), Free University of Brussels (VUB), Pleinlaan 2, B-1050 Brussels, Belgium, Department of Chemistry, Universiteit Antwerpen, Universiteitsplein 1, B-2610 Antwerpen
| | - W. Langenaeker
- Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S-3), B-9000 Gent, Belgium, Molecular Design and Chemoinformatics, Johnson & Johnson Pharmaceutical Research and Development, Turnhoutseweg 30, B-2340 Beerse, Belgium, European Patent Office, Bayerstrasse 34, D-80335 Munich, Germany, Eenheid Algemene Chemie (ALGC), Free University of Brussels (VUB), Pleinlaan 2, B-1050 Brussels, Belgium, Department of Chemistry, Universiteit Antwerpen, Universiteitsplein 1, B-2610 Antwerpen
| | - P. Lahorte
- Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S-3), B-9000 Gent, Belgium, Molecular Design and Chemoinformatics, Johnson & Johnson Pharmaceutical Research and Development, Turnhoutseweg 30, B-2340 Beerse, Belgium, European Patent Office, Bayerstrasse 34, D-80335 Munich, Germany, Eenheid Algemene Chemie (ALGC), Free University of Brussels (VUB), Pleinlaan 2, B-1050 Brussels, Belgium, Department of Chemistry, Universiteit Antwerpen, Universiteitsplein 1, B-2610 Antwerpen
| | - F. De Proft
- Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S-3), B-9000 Gent, Belgium, Molecular Design and Chemoinformatics, Johnson & Johnson Pharmaceutical Research and Development, Turnhoutseweg 30, B-2340 Beerse, Belgium, European Patent Office, Bayerstrasse 34, D-80335 Munich, Germany, Eenheid Algemene Chemie (ALGC), Free University of Brussels (VUB), Pleinlaan 2, B-1050 Brussels, Belgium, Department of Chemistry, Universiteit Antwerpen, Universiteitsplein 1, B-2610 Antwerpen
| | - P. Geerlings
- Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S-3), B-9000 Gent, Belgium, Molecular Design and Chemoinformatics, Johnson & Johnson Pharmaceutical Research and Development, Turnhoutseweg 30, B-2340 Beerse, Belgium, European Patent Office, Bayerstrasse 34, D-80335 Munich, Germany, Eenheid Algemene Chemie (ALGC), Free University of Brussels (VUB), Pleinlaan 2, B-1050 Brussels, Belgium, Department of Chemistry, Universiteit Antwerpen, Universiteitsplein 1, B-2610 Antwerpen
| | - C. Van Alsenoy
- Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S-3), B-9000 Gent, Belgium, Molecular Design and Chemoinformatics, Johnson & Johnson Pharmaceutical Research and Development, Turnhoutseweg 30, B-2340 Beerse, Belgium, European Patent Office, Bayerstrasse 34, D-80335 Munich, Germany, Eenheid Algemene Chemie (ALGC), Free University of Brussels (VUB), Pleinlaan 2, B-1050 Brussels, Belgium, Department of Chemistry, Universiteit Antwerpen, Universiteitsplein 1, B-2610 Antwerpen
| | - J. P. Tollenaere
- Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S-3), B-9000 Gent, Belgium, Molecular Design and Chemoinformatics, Johnson & Johnson Pharmaceutical Research and Development, Turnhoutseweg 30, B-2340 Beerse, Belgium, European Patent Office, Bayerstrasse 34, D-80335 Munich, Germany, Eenheid Algemene Chemie (ALGC), Free University of Brussels (VUB), Pleinlaan 2, B-1050 Brussels, Belgium, Department of Chemistry, Universiteit Antwerpen, Universiteitsplein 1, B-2610 Antwerpen
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Bultinck P, Langenaeker W, Lahorte P, De Proft F, Geerlings P, Waroquier M, Tollenaere JP. The Electronegativity Equalization Method I: Parametrization and Validation for Atomic Charge Calculations. J Phys Chem A 2002. [DOI: 10.1021/jp0205463] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- P. Bultinck
- Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S-3), B-9000 Gent, Belgium, Molecular Design and Chemoinformatics, Johnson & Johnson Pharmaceutical Research and Development, Turnhoutseweg 30, B-2340 Beerse, Belgium, European Patent Office, Bayerstrasse 34, D-80335 Munich, Germany, Eenheid Algemene Chemie (ALGC), Free University of Brussels (VUB), Pleinlaan 2, B-1050 Brussels, Belgium, Laboratory of Theoretical Physics, Ghent University, Proeftuinstraat 86, B-9000 Gent,
| | - W. Langenaeker
- Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S-3), B-9000 Gent, Belgium, Molecular Design and Chemoinformatics, Johnson & Johnson Pharmaceutical Research and Development, Turnhoutseweg 30, B-2340 Beerse, Belgium, European Patent Office, Bayerstrasse 34, D-80335 Munich, Germany, Eenheid Algemene Chemie (ALGC), Free University of Brussels (VUB), Pleinlaan 2, B-1050 Brussels, Belgium, Laboratory of Theoretical Physics, Ghent University, Proeftuinstraat 86, B-9000 Gent,
| | - P. Lahorte
- Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S-3), B-9000 Gent, Belgium, Molecular Design and Chemoinformatics, Johnson & Johnson Pharmaceutical Research and Development, Turnhoutseweg 30, B-2340 Beerse, Belgium, European Patent Office, Bayerstrasse 34, D-80335 Munich, Germany, Eenheid Algemene Chemie (ALGC), Free University of Brussels (VUB), Pleinlaan 2, B-1050 Brussels, Belgium, Laboratory of Theoretical Physics, Ghent University, Proeftuinstraat 86, B-9000 Gent,
| | - F. De Proft
- Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S-3), B-9000 Gent, Belgium, Molecular Design and Chemoinformatics, Johnson & Johnson Pharmaceutical Research and Development, Turnhoutseweg 30, B-2340 Beerse, Belgium, European Patent Office, Bayerstrasse 34, D-80335 Munich, Germany, Eenheid Algemene Chemie (ALGC), Free University of Brussels (VUB), Pleinlaan 2, B-1050 Brussels, Belgium, Laboratory of Theoretical Physics, Ghent University, Proeftuinstraat 86, B-9000 Gent,
| | - P. Geerlings
- Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S-3), B-9000 Gent, Belgium, Molecular Design and Chemoinformatics, Johnson & Johnson Pharmaceutical Research and Development, Turnhoutseweg 30, B-2340 Beerse, Belgium, European Patent Office, Bayerstrasse 34, D-80335 Munich, Germany, Eenheid Algemene Chemie (ALGC), Free University of Brussels (VUB), Pleinlaan 2, B-1050 Brussels, Belgium, Laboratory of Theoretical Physics, Ghent University, Proeftuinstraat 86, B-9000 Gent,
| | - M. Waroquier
- Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S-3), B-9000 Gent, Belgium, Molecular Design and Chemoinformatics, Johnson & Johnson Pharmaceutical Research and Development, Turnhoutseweg 30, B-2340 Beerse, Belgium, European Patent Office, Bayerstrasse 34, D-80335 Munich, Germany, Eenheid Algemene Chemie (ALGC), Free University of Brussels (VUB), Pleinlaan 2, B-1050 Brussels, Belgium, Laboratory of Theoretical Physics, Ghent University, Proeftuinstraat 86, B-9000 Gent,
| | - J. P. Tollenaere
- Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S-3), B-9000 Gent, Belgium, Molecular Design and Chemoinformatics, Johnson & Johnson Pharmaceutical Research and Development, Turnhoutseweg 30, B-2340 Beerse, Belgium, European Patent Office, Bayerstrasse 34, D-80335 Munich, Germany, Eenheid Algemene Chemie (ALGC), Free University of Brussels (VUB), Pleinlaan 2, B-1050 Brussels, Belgium, Laboratory of Theoretical Physics, Ghent University, Proeftuinstraat 86, B-9000 Gent,
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37
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van Duin ACT, Dasgupta S, Lorant F, Goddard WA. ReaxFF: A Reactive Force Field for Hydrocarbons. J Phys Chem A 2001. [DOI: 10.1021/jp004368u] [Citation(s) in RCA: 3615] [Impact Index Per Article: 157.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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38
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Smirnov KS. Computer Modeling Study of Interaction of Acetonitrile with Hydroxyl Groups of HY Zeolite. J Phys Chem B 2001. [DOI: 10.1021/jp004345f] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Konstantin S. Smirnov
- Laboratory for Applied Organic Chemistry and Catalysis, Delft University of Technology, Julianalaan 136, 2628 BL Delft, The Netherlands, and Laboratoire de Spectrochimie Infrarouge et Raman du CNRS, Bâtiment C5, Université des Sciences et Technologies de Lille, 59655 Villeneuve d'Ascq, Cedex, France
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39
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Clark LA, Ellis DE, Snurr RQ. A Fukui function overlap method for predicting reactivity in sterically complex systems. J Chem Phys 2001. [DOI: 10.1063/1.1338977] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Smirnov KS, Thibault-Starzyk F. Confinement of Acetonitrile Molecules in Mordenite. A Computer Modeling Study. J Phys Chem B 1999. [DOI: 10.1021/jp991520n] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Konstantin S. Smirnov
- Laboratoire Catalyse et Spectrochimie, CNRS-Institut des Sciences de la Matière et du Rayonnement, 6 Boulevard du Maréchal Juin, 14050 Caen Cedex, France
| | - Frédéric Thibault-Starzyk
- Laboratoire Catalyse et Spectrochimie, CNRS-Institut des Sciences de la Matière et du Rayonnement, 6 Boulevard du Maréchal Juin, 14050 Caen Cedex, France
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