Review
Chemistry, Multidisciplinary
Kevin Carter-Fenk, Ka Un Lao, John M. Herbert
Summary: Non-covalent forces are essential in molecular interactions. Symmetry-adapted perturbation theory (SAPT) provides an accurate method to calculate these interactions, decomposing the energy into meaningful components and aiding in the construction of transferable force fields.
ACCOUNTS OF CHEMICAL RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Li Tang, Weihua Zhu
Summary: A series of new high-energy insensitive compounds were designed based on the RDX skeleton, with their properties analyzed and predicted using DFT. One compound with excellent performance was found to have superior detonation properties and lower impact sensitivity. The study demonstrates the potential for developing novel energetic compounds through incorporating intermolecular linkages in bicyclic or cage compounds based on the RDX framework.
Article
Chemistry, Physical
Sirous Yourdkhani, Jiri Klimes
Summary: The projector-augmented wave (PAW) method is widely used to speed up electronic structure calculations. This study shows that interaction energies of molecular dimers can be used to identify problematic PAW data sets and understand the errors. A simple scheme is proposed to correct the errors and reduce the interaction energy errors.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Multidisciplinary Sciences
Laura Schaedel, Charlotta Lorenz, Anna V. Schepers, Stefan Klumpp, Sarah Koester
Summary: The study demonstrates that vimentin intermediate filaments stabilize microtubules against depolymerization and support microtubule rescue through direct interactions in a reconstituted in vitro system. By measuring interaction forces and numerical simulations, insights into the physical nature of these interactions and their effects on microtubule dynamics are provided.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Jose Eduardo Zamudio Diaz Miron, Matthias Stein
Summary: Organometallic complexes play important roles in homogeneous catalysis, materials science, and pharmaceuticals. The interaction between these complexes in the solid state determines their properties and availability. Non-covalent interactions are crucial for stabilizing the crystals of transition metal complexes. Assessing the consistency between experimental and computational data is essential for further method development and crystal engineering.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Yao-Wen Chang, Yia-Chung Chang
Summary: This work studied trions in two-dimensional space using the variational method, calculating trion energy levels and wavefunctions efficiently and accurately. Results showed that ground-state trions are bound in all parameter ranges, while excited-state trions with finite angular momentum can also be bound in certain scenarios. Additionally, electron-hole exchange interaction was found to significantly impact trion binding energies and the potential existence of stable excited-state trions in transition metal dichalcogenides.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Piyush Panini, Eline Boel, Luc Van Meervelt, Guy Van den Mooter
Summary: The phenomenon of solvatomorphism in drugs has significant implications in the pharmaceutical industry and crystal engineering. This study presents the crystal structure of Miconazole and its solvates, along with a detailed analysis of their packing using various methods.
CRYSTAL GROWTH & DESIGN
(2022)
Article
Chemistry, Physical
Caio L. Firme
Summary: The local potential energy density model, LPE, exhibits high linearity with the supramolecular binding energy, SME, and can be used to predict the SME of various inter/intramolecular interactions. However, LPE is sensitive to dispersion and electrostatic components, with polarization component having a significant impact on its accuracy.
COMPUTATIONAL AND THEORETICAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Kenneth B. Wiberg
Summary: For methyl halides and phenyl halides, the 90 degrees approach leads to 1-2 kcal/mol stabilization due to halogen hydrogen interactions. The best arrangement for chlorobenzene dimer is with two benzene rings oriented over each other, with meta orientation of the chlorines having a lower energy. The dimerization energy suggests that the effect of the halogen on the electron distribution is more important than Cl center dot center dot center dot Cl interaction.
Article
Chemistry, Multidisciplinary
Fionn D. Malone, Robert M. Parrish, Alicia R. Welden, Thomas Fox, Matthias Degroote, Elica Kyoseva, Nikolaj Moll, Raffaele Santagati, Michael Streif
Summary: We have developed a simple and efficient method for calculating interaction energies between large molecular systems using symmetry-adapted perturbation theory (SAPT) and the variational quantum eigensolver (VQE). The SAPT(VQE) method achieves high accuracy and reduces the quantum requirements.
Article
Chemistry, Physical
Kimihiko Hirao, Takahito Nakajima, Bun Chan
Summary: The study extended Slater's transition state concept to approximate total energy differences using three orbital energies; numerical validation showed accurate reproduction of Delta SCF values; while the current method has some limitations, it contributes to an improved understanding of SCF-type orbital theories.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Biochemistry & Molecular Biology
Alfonso Ferretti, Laura Canal, Robert A. Sorodoc, Sourab Sinha, Giuseppe Brancato
Summary: Dispersion-inclusive density functional theory (DFT) methods have shown improved performances compared to standard DFT approximations for modeling large molecular systems, although disagreements with reference calculations still exist. Applying general-purpose corrections, such as Grimme's DFT-D models, can lead to inconsistent results, recommending careful evaluation. In this study, a simple optimization protocol is proposed to enhance the accuracy of DFT-D methods for modeling water clusters, achieving remarkable agreement with accurate MC intermolecular interactions.
Article
Engineering, Environmental
Qi Sun, Ning Ding, Chaofeng Zhao, Jie Ji, Shenghua Li, Siping Pang
Summary: The effective strategy based on positional isomerism has been proposed to enhance the density of energetic materials and led to the synthesis of a high-density nitramino compound 2 with improved detonation performance compared to the original material 1.
CHEMICAL ENGINEERING JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Jia-Rui Wu, Dongxia Li, Gengxin Wu, Meng-Hao Li, Ying-Wei Yang
Summary: This study develops a strategy to modulate supramolecular ICT interactions in the solid state by compressing the binding cavity of a macrocyclic host, leading to improved affinities with electron-deficient planar guests.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemistry & Molecular Biology
Yunxian Ma, Ruixi Chen, Zidi Chen, Zhipeng Wang, Jinfeng Chen, Shenggui Zhang
Summary: Intermolecular interactions between vanillic acid and porous starch were investigated using solid-state NMR, and their effects on digestibility were evaluated. The results showed that the formation of ester bonds indicated the presence of covalent interactions between VA and PS. The VA-PS conjugate, characterized by stronger covalent interactions, exhibited superior effects in inhibiting starch digestibility compared with non-covalent interactions.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Chemistry, Multidisciplinary
Xavier Deraet, Jan Turek, Mercedes Alonso, Frederik Tielens, Stefaan Cottenier, Paul W. Ayers, Bert M. Weckhuysen, Frank De Proft
Summary: The study focused on single-atom catalysis using density functional theory, revealing the sensitivity of silver and gold atoms to van der Waals dispersion forces, and the role of oxophilicity in the interaction strength of late transition metals on the SiO2 support. Adsorption energies varied between -1.40 to -1.92 eV for row 4 elements, and between -2.20 to -2.92 eV for heavier metals, except for Pd. The Fermi weighted density of states approach was identified as the most suitable for describing reactivity trends and showed good agreement with experimental data.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Ruben Laplaza, Carlos Cardenas, Patrick Chaquin, Julia Contreras-Garcia, Paul W. Ayers
Summary: Dynamical orbital forces, derived from conceptual DFT, can interpret the results of routine ab initio calculations in terms of forces and occupations, as shown in this work. The approach is validated numerically for valence orbitals in Kohn-Sham DFT and showcased its usefulness in applications in aromatic and antiaromatic systems and in excited state chemistry.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2021)
Article
Chemistry, Physical
Qin Wu, Guangjin Wang, Mingjie Liu
Summary: This study reveals that the sensitivity of CO binding strengths in different transition metal atoms on nitrogen-doped graphene to DFT methods varies significantly, depending on different local spin configurations. Caution is necessary when using DFT binding energies for quantitative predictions in TM/NG single atom catalysis.
Article
Chemistry, Physical
Leila Pujal, Maximilian Van Zyl, Esteban Voehringer-Martinez, Toon Verstraelen, Patrick Bultinck, Paul W. Ayers, Farnaz Heidar-Zadeh
Summary: This article presents a variational procedure for the iterative Hirshfeld partitioning scheme, which provides a formal and straightforward approach for imposing constraints when computing atomic properties. The constrained iterative Hirshfeld method shows promising results in calculating atomic properties with added constraints.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Computer Science, Interdisciplinary Applications
Fanwang Meng, Michael Richer, Alireza Tehrani, Jonathan La, Taewon David Kim, Paul W. Ayers, Farnaz Heidar-Zadeh
Summary: Procrustes is a free, open-source, cross-platform Python library that implements various algorithmic solutions to Procrustes problems, aiming to find an optimal transformation that makes two matrices as close as possible. It has broad applicability in fields such as cheminformatics, image recognition, signal processing, data science, machine learning, computational biology, chemistry, and physics.
COMPUTER PHYSICS COMMUNICATIONS
(2022)
Article
Chemistry, Physical
Qin Wu, Talin Avanesian, Xiaohui Qu, Hubertus Van Dam
Summary: PolyODENet is a program that uses machine learning methods to derive kinetic differential equations and predicts concentrations at arbitrary time points. It can apply physical constraints and chemical knowledge to regularize the solution space, revealing hidden parts of reaction mechanisms.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Stijn Fias, Paul W. Ayers, Frank De Proft, Paul Geerlings
Summary: This article provides an overview of the mathematical properties of non-local second order derivatives in various ensembles and discusses their significance for atoms and molecules. The article also explores other interesting properties derived from these properties and proposes practical strategies for calculating these kernel functions and their eigenvalues.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Taewon D. Kim, M. Richer, Gabriela Sanchez-Diaz, Ramon Alain Miranda-Quintana, Toon Verstraelen, Farnaz Heidar-Zadeh, Paul W. Ayers
Summary: Fanpy is a Python library for developing and testing multideterminant wavefunctions and related ab initio methods in electronic structure theory. It simplifies the process of converting mathematical formulations into working implementations and allows for quick prototyping of new methods. Fanpy is based on the FANCI framework and represents multideterminant wavefunctions using overlaps with Slater determinants. It is modular in structure, allowing for the combination of different methods and compatibility with various operating systems.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Yilin Zhao, Dongbo Zhao, Xin He, Paul W. W. Ayers, Shubin Liu
Summary: Accurately predicting the polarizabilities of macromolecules is a challenging problem. This study uses simple density-based quantities from the information-theoretic approach to predict the polarizability of proteins. The applicability of these quantities for predicting polarizability in inorganic, organic, and biological systems with different electronic structures is verified. The proposed GEBF-ITA protocol combines the information-theoretic approach with the linear-scaling generalized energy-based fragmentation method to predict the polarizability of macromolecules, providing an inexpensive yet accurate theoretical tool.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Bin Wang, Paul Geerlings, Christian Van Alsenoy, Farnaz Heider-Zadeh, Paul W. Ayers, Frank De Proft
Summary: The linear response function has been successful in time-dependent density functional theory, but its application in chemical reactivity has received less attention. In this work, the robustness of the linear response function is assessed at different approximation levels. The independent particle approximation yields qualitatively correct results, but for quantitative results, the inclusion of Coulomb and exchange-correlation terms is necessary.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Biochemistry & Molecular Biology
Dongbo Zhao, Xin He, Paul W. Ayers, Shubin Liu
Summary: Accurately and efficiently determining the polarizabilities of excited states is a challenge in both experimental and computational studies. This research demonstrates that density-based functions can be used to predict excited-state polarizabilities and verifies their correlation and predictability through experiments.
Article
Chemistry, Physical
Xin He, Tian Lu, Chunying Rong, Shubin Liu, Paul W. Ayers, Wenjian Liu
Summary: Considerable research interest has been observed in recent literature regarding the development and applications of information-theoretic approach (ITA) quantities in density functional theory. These ITA quantities are explicit density functionals with continuous and well-behaved local distributions in real space. By systematically analyzing the topological behavior of four representative ITA quantities, namely Shannon entropy, two forms of Fisher information, and relative Shannon entropy, our work further develops ITA. The topological analyses for 103 molecular systems provide new insights into bonding interactions and physiochemical properties, such as electrophilicity, nucleophilicity, acidity, and aromaticity. Comparisons with results from other functions demonstrate the potential of our results as a methodological approach and practical tool for elucidating chemical bonding and reactivity propensity.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Alireza Tehrani, James S. M. Anderson, Debajit Chakraborty, Juan I. Rodriguez-Hernandez, David C. Thompson, Toon Verstraelen, Paul W. Ayers, Farnaz Heidar-Zadeh
Summary: The numerical ill-conditioning of approximating electron density with convex sums of Gaussian or Slater-type functions is solved using the (extended) Kullback-Leibler divergence. The optimized densities are accurate for molecular similarity, electron density topology, and numerical molecular integration applications. This robust approach can fit any non-negative normalized functions to convex sums of non-negative basis functions and is compared to gradient-based optimization methods using a fixed-point iteration method.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Mesfin Diro Chaka, Chernet Amente Geffe, Alex Rodriguez, Nicola Seriani, Qin Wu, Yedilfana Setarge Mekonnen
Summary: Redox flow batteries (RFBs) are a promising option for large-scale energy storage due to their high energy density, low cost, and environmental benefits. However, identifying organic compounds with the desired properties for RFB technology is a challenging task. In this study, a graph neural network-based model called MolGAT was developed to predict the redox potential of organic molecules using their molecular structures, atomic properties, and bond attributes.
Article
Chemistry, Physical
Andrew M. Teale, Trygve Helgaker, Andreas Savin, Carlo Adamo, Balint Aradi, Alexei Arbuznikov, Paul W. Ayers, Evert Jan Baerends, Vincenzo Barone, Patrizia Calaminici, Eric Cances, Emily A. Carter, Pratim Kumar Chattaraj, Henry Chermette, Ilaria Ciofini, T. Daniel Crawford, Frank De Proft, John F. Dobson, Claudia Draxl, Thomas Frauenheim, Emmanuel Fromager, Patricio Fuentealba, Laura Gagliardi, Giulia Galli, Jiali Gao, Paul Geerlings, Nikitas Gidopoulos, Peter M. W. Gill, Paola Gori-Giorgi, Andreas Gorling, Tim Gould, Stefan Grimme, Oleg Gritsenko, Hans Jorgen Aagaard Jensen, Erin R. Johnson, Robert O. Jones, Martin Kaupp, Andreas M. Koster, Leeor Kronik, Anna Krylov, Simen Kvaal, Andre Laestadius, Mel Levy, Mathieu Lewin, Shubin Liu, Pierre-Francois Loos, Neepa T. Maitra, Frank Neese, John P. Perdew, Katarzyna Pernal, Pascal Pernot, Piotr Piecuch, Elisa Rebolini, Lucia Reining, Pina Romaniello, Adrienn Ruzsinszky, Dennis R. Salahub, Matthias Scheffler, Peter Schwerdtfeger, Viktor N. Staroverov, Jianwei Sun, Erik Tellgren, David J. Tozer, Samuel B. Trickey, Carsten A. Ullrich, Alberto Vela, Giovanni Vignale, Tomasz A. Wesolowski, Xin Xu, Weitao Yang
Summary: This paper provides an informal review and discussion on the history, present status, and future of density-functional theory (DFT) by 70 workers in the field. The format of a roundtable discussion allowed participants to express their views through 302 individual contributions to a preset list of 26 questions. Supported by a bibliography of 777 entries, the paper offers a comprehensive snapshot of DFT in 2022.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)