Article
Biochemistry & Molecular Biology
Krzysztof Szalewicz, Bogumil Jeziorski
Summary: SAPT is a method for computational studies of noncovalent interactions, providing clear physical interpretations and specific dependence on intermolecular separation. It connects interaction energies with monomers' properties through the asymptotic multipole expansion.
JOURNAL OF MOLECULAR MODELING
(2022)
Article
Chemistry, Physical
Bonis Barcza, Adam B. Szirmai, Attila Tajti, John F. Stanton, Peter G. Szalay
Summary: Although Coupled-Cluster methods accurately describe excited electronic states, their computational costs limit their application. This study focuses on fragment-based approaches for noncovalently bound molecular complexes with interacting chromophores. Two approaches were tested for describing the states localized on the fragments with electrostatic interactions, Pauli repulsion, and dispersion effects. The effective fragment potential method was found to provide an adequate correction. Electrostatic contributions were sufficient for modeling the interaction of the localized chromophores.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Isolde Sandler, Shaleen Sharma, Bun Chan, Junming Ho
Summary: This study used contemporary methods to predict gas-phase anion binding energies, finding M06-2X as the best performing method, with other methods showing systematic errors that increase with the degree of carbonylation of the receptors.
JOURNAL OF PHYSICAL CHEMISTRY A
(2021)
Article
Chemistry, Physical
Kevin Carter-Fenk, John M. Herbert
Summary: In this study, we propose improvements to the dispersion damping potentials in the effective fragment potential (EFP) and evaluate their performance using a new database of ionic liquid constituents. We recommend a new parameter-free dispersion damping function as a replacement for the current one used in EFP.
Article
Chemistry, Physical
T. P. Straatsma, R. Broer, A. Sanchez-Mansilla, C. Sousa, C. de Graaf
Summary: GronOR is a program package designed for nonorthogonal configuration interaction calculations, particularly for large molecular assemblies. It utilizes massively parallel supercomputer architectures and accelerator technologies, with considerations for fault resiliency and heterogeneous computing. The software is open source and can run effectively on small clusters and workstations as well.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
F. Zahariev, M. S. Gordon
Summary: The previously developed combined Quantum Monte Carlo-Effective Fragment Molecular Orbital (QMC-EFMO) method has been extended to systems where the fragmentation process cuts across covalent molecular bonds. The extended QMC-EFMO capability was demonstrated on several model systems with good agreement between full QMC and QMC-EFMO for both the correlation energy and energy differences. The differences were within 2 kcal mol(-1) and 1 kcal mol(-1) respectively.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Multidisciplinary Sciences
Jishnunil Chakraborty
Summary: This study investigates the nature of weak noncovalent interactions in the self-assembled dimers of two metal complexes using density functional theory. The results provide insights into the structural patterns and physical components of interaction energies, and further analysis is conducted using absorption spectra and reactivity parameters.
Article
Chemistry, Physical
Ehsan Masumian, A. Daniel Boese
Summary: This study investigates the role of pi-resonance in the enhancement of intramolecular hydrogen bonds (IMHBs) by comparing pi-conjugated systems to their saturated planar counterparts. The results show that pi-resonance primarily affects the induction and electrostatics contributions to the IMHB energies. The stabilization of IMHBs is achieved by reducing the repulsion caused by the exchange term. These findings are consistent with expected trends in resonance assisted hydrogen bonds (RAHBs) and validate the fragmentation procedures used in this study.
Article
Chemistry, Physical
Jeffrey B. Schriber, Dominic A. Sirianni, Daniel G. A. Smith, Lori A. Burns, Doree Sitkoff, Daniel L. Cheney, C. David Sherrill
Summary: The Symmetry-adapted perturbation theory (SAPT) is a valuable tool for studying non-covalent interactions, but its computational cost can be reduced by replacing dispersion terms. The SAPT0-D3 method improves accuracy and efficiency, with the addition of functional group partitioning for analyzing binding interactions.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Moritz Thurlemann, Sereina Riniker
Summary: Electronic structure methods offer accurate predictions but with high computational costs. Empirical methods are cheaper but have inherent approximations and data dependence. Machine learning force fields exacerbate limitations related to training data. A proposed hybrid model combines machine learning and classical force fields, providing accuracy and flexibility.
Article
Chemistry, Multidisciplinary
Eugene A. Katlenok, Anton Rozhkov, Oleg Levin, Matti Haukka, Maxim L. Kuznetsov, Vadim Yu Kukushkin
Summary: This study investigated the crystal structures of Pd-2(II) half-lantern complexes and cocrystals through X-ray crystallography, revealing the significant roles played by various noncovalent interactions such as I···Pd and I···E.
CRYSTAL GROWTH & DESIGN
(2021)
Article
Chemistry, Physical
Viki Kumar Prasad, Alberto Otero-de-la-Roza, Gino A. DiLabio
Summary: In this study, a new low-cost quantum mechanical method using atom-centered potentials (ACPs) was developed to model large molecular systems. Machine learning regression technique was utilized to train and validate the ACP-corrected methods. The proposed ACP-corrected methods showed comparable performance to complete basis set density functional theory at a much lower cost, and could improve the description of covalent and noncovalent bond geometries.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Francisco Ballesteros, Shelbie Dunivan, Ka Un Lao
Summary: This work reports benchmark binding energies for dispersion-bound complexes, DNA-ellipticine intercalation complex, and buckycatcher-C-60 complex with 120 heavy atoms using a focal-point method based on MP2 and CCSD(T) extrapolated to the CBS limit. The discrepancies between CCSD(T) and fixed-node diffusion Monte Carlo methods are substantial for large noncovalent complexes.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Multidisciplinary Sciences
Yasmine S. Al-Hamdani, Peter R. Nagy, Andrea Zen, Dennis Barton, Mihaly Kallay, Jan Gerit Brandenburg, Alexandre Tkatchenko
Summary: Quantum-mechanical methods are widely employed for describing molecular interactions, but discrepancies between CCSD(T) and DMC interaction energies for a set of polarizable supramolecules call for further collaborative efforts to resolve this issue.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Thomas Gasevic, Julius B. Stueckrath, Stefan Grimme, Markus Bursch
Summary: The Swiss army knife composite density functional electronic-structure method r(2)SCAN-3c has been extended and optimized for the use with Slater-type orbital basis sets. The performance of the new implementation has been assessed on various benchmark sets, showing that it is on par with or more accurate than other methods in geometry optimizations and has similar overall accuracy in energy calculations. The STO-based r(2)SCAN-3c outperforms many conventional methods in common applications at a lower cost.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Article
Chemistry, Physical
Aria J. Bredt, Yongbin Kim, Denilson Mendes de Oliveira, Andres S. Urbina, Lyudmila Slipchenko, Dor Ben-Amotz
Summary: This study evaluates the affinity of hydroxide ions for methyl hydration shells through experimental and simulation analysis, and reveals that hydroxide ions are more strongly expelled from the methyl group hydration shells compared to iodide ions, with their distribution correlated with sodium counterion localization near the TBA hydroxyl group.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Physical
Dominic A. Sirianni, Xiao Zhu, Doree F. Sitkoff, Daniel L. Cheney, C. David Sherrill
Summary: High-level quantum chemical computations provide significant insight into the nature of non-covalent interactions. Previous studies have mainly focused on gas-phase computations, but non-covalent interactions frequently occur in complex chemical environments. This study examines the pi-pi interactions in an aqueous solution and analyzes how the solvent molecules affect these interactions. The results show that the nearby solvent molecules have little effect on the direct solute-solute interactions, except for charged solutes, indicating that the differences in binding energies between the gas phase and solution phase are primarily due to the competition between solute-solute and solute-solvent interactions.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Dmitri Kosenkov
Summary: Excitation energy transfer is a widespread process with fundamental importance in understanding natural phenomena and advancing technologies. PyFREC 2.0 is a computational tool based on Forster theory that aids in understanding the photochemical mechanisms of fluorescence resonance energy transfer (FRET).
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2022)
Article
Chemistry, Physical
Derek P. Metcalf, Andrew Smith, Zachary L. Glick, C. David Sherrill
Summary: This study assesses the range-dependent character of two-body interactions in 24 small organic molecular crystals, providing guidance for estimating convergence rates in other molecular crystals.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Yi Xie, Daniel G. A. Smith, C. David Sherrill
Summary: This study presents an implementation of a symmetry-adapted perturbation theory algorithm based on density functional theory, utilizing density-fitting treatment of hybrid exchange-correlation kernels for describing monomers with hybrid functionals. The algorithm shows improved numerical stability and computational efficiency, performing well for systems with up to 3000 basis functions.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Yuichiro Watanabe, Benjamin M. Washer, Matthias Zeller, Sergei Savikhin, Lyudmila Slipchenko, Alexander Wei
Summary: This study describes a novel manifestation of rigidochromic behavior in a series of tetranuclear Cu(I)-pyrazolate macrocycles, with implications for solid-state luminescence. The findings reveal that the structural effects far from the luminescent core significantly impact the emissions, with the addition of a C4 substituent inducing a blue shift. Additionally, the emissions are primarily mediated through a cluster-centered triplet state.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Physical
Caroline T. Sargent, Derek P. Metcalf, Zachary L. Glick, Carlos H. Borca, C. David Sherrill
Summary: Using the many-body expansion method, we predicted crystal lattice energies (CLEs) with flexibility in theoretical methods. We computed two-body contributions of 23 molecular crystals using different quantum chemical levels and compared them with coupled-cluster in the complete basis set (CBS) limit. Accurate calculations were achieved for interaction energies of distant dimers using certain methods, reducing the computational expense of coupled-cluster by up to 98%.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Medicinal
Rameshwar L. Kumawat, C. David Sherrill
Summary: High-order quantum chemistry methods were used to study the intermolecular interaction energies and their components for hydrogen-bonded DNA nucleobase pairs and non-natural Hachimoji nucleobase pairs. The most attractive component of the interaction energies was found to be the electrostatic interactions, followed closely by the sum of induction/polarization and London dispersion. Non-natural Hachimoji base pairs exhibited stronger interactions than the corresponding natural base pairs, while the natural base pairs were more stabilized in their Hoogsteen geometries. Hoogsteen geometries were less favorable for non-natural Hachimoji base pairs compared to Watson-Crick geometries.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Editorial Material
Chemistry, Physical
Michele Ceriotti, Lasse Jensen, David E. Manolopoulos, Todd Martinez, David R. Reichman, Francesco Sciortino, C. David Sherrill, Qiang Shi, Carlos Vega, Lai-Sheng Wang, Emily A. Weiss, Xiaoyang Zhu, Jenny Stein, Tianquan Lian
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Carlos H. Borca, Zachary L. Glick, Derek P. Metcalf, Lori A. Burns, C. David Sherrill
Summary: The use of many-body expansion (MBE) method, combining CCSD(T)/CBS for closest dimers and trimers and MP2 for more distant ones, shows promising results in efficiently calculating lattice energies in organic crystals. The effectiveness of MP2(+ATM) as a replacement for CCSD(T)/CBS is demonstrated. The CCSD(T)/CBS best estimate of the lattice energy at 0 K is -54.01 kJ mol(-1).
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Yi Xie, Zachary L. L. Glick, C. David Sherrill
Summary: This study investigates the three-body dispersion contribution to crystal lattice energies in benzene, carbon dioxide, and triazine. By using various computational methods, it is observed that these contributions converge rapidly with increasing intermolecular distances. The closest-contact distance, R-min, shows a strong correlation with the three-body contribution, while R-max is used as a cutoff criterion for considering the number of trimers. The results suggest that the MP2+ATM method can be used to compute trimers with R-min > 4 angstrom to reduce computational cost.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Christopher P. West, Daniela Mesa Sanchez, Ana C. Morales, Yun-Jung Hsu, Jackson Ryan, Andrew Darmody, Lyudmila V. Slipchenko, Julia Laskin, Alexander Laskin
Summary: This study utilizes ion mobility spectrometry with mass spectrometry detection to separate and characterize biogenic secondary organic aerosols (SOAs), revealing differences in chemical composition and molecular structure between different emission sources and aging processes in the atmosphere. The collision cross sections and structural features of monomeric and dimeric SOA components were determined through gas-phase separation and structural calculations. The study also highlights the impact of ionization mode on the collision cross section values, with Na+-coordinated oligomeric ions showing more compact structures and deprotonated molecules exhibiting elongated structures.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Physical
Patrick K. Wise, Lyudmila V. Slipchenko, Dor Ben-Amotz
Summary: The adsorption of ionic and neutral spherical solutes on a liquid water droplet surface was investigated in this study through molecular dynamics simulations and theoretical analyses. The results showed a change in the adsorption free energy sign based on the size of ions, with larger ions exhibiting increased surface activity. The adsorption free energies were decomposed into energetic and entropic contributions, with larger ions being driven by entropy while smaller ions were affected by a delicate balance of energetic and entropic factors. The findings have implications for interfacial acidity and enhanced chemical reactivity.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Physical
Philip M. Nelson, Zachary L. Glick, C. David Sherrill
Summary: The focal-point approximation combines multiple lower-accuracy, faster computations to estimate a high-accuracy, slow quantum chemistry computation. By combining MP2 with CCSD(T) methods, the focal-point CCSD(T) method can approach the complete basis set (CBS) limit with only triple-xi basis sets. Compared with experimental values, the predicted harmonic and fundamental frequencies using the focal-point method have smaller mean absolute errors, and the computation time required is much less, especially for larger molecules.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Multidisciplinary Sciences
Steven A. Spronk, Zachary L. Glick, Derek P. Metcalf, C. David Sherrill, Daniel L. Cheney
Summary: Fast and accurate calculation of intermolecular interaction energies is crucial for understanding chemical and biological processes. The Splinter dataset, which contains paired molecular fragments representing common substructures in proteins and small-molecule ligands, has been created to facilitate the development and improvement of computational methods for performing these calculations. It is expected to serve as a benchmark dataset for training and testing various methods for calculating intermolecular interaction energies.