Article
Biochemistry & Molecular Biology
Dooam Paik, Hankyul Lee, Hyungjun Kim, Jeong-Mo Choi
Summary: The pi-pi interaction is a major driving force in protein folding and liquid-liquid phase separation. Our computational study of the solvation effect on pi-pi interactions in water reveals that solvation influences the association free energies of benzene and phenol dimers, but not significantly when no direct hydrogen-bond-type interaction exists between two monomeric units.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Hiromi Oshita, Yuichi Shimazaki
Summary: The pi-pi stacking interaction is a weak interaction that plays an important role in protein structure stabilization and functionalization. This article discusses the effect of the pi-pi stacking interaction between alkylthio-substituted phenoxyl radical and an indole ring.
Article
Chemistry, Inorganic & Nuclear
Ping Yu, Dan Peng, Li-Hua He, Jing-Lin Chen, Jin-Yun Wang, Sui-Jun Liu, He-Rui Wen
Summary: The study explores a stimuli-responsive cuprous luminescent complex with two crystalline polymorphs demonstrating distinct emissions, shedding light on the relationship between mechanochromic luminescence and intramolecular π···π interactions and geometrical configuration. Results suggest the rational utilization of switchable intramolecular π···π interactions as a feasible approach for developing stimuli-responsive intelligent luminescent materials and devices.
INORGANIC CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Yujie Zhu, Minmin Tang, Huibin Zhang, Faiz-Ur Rahman, Pablo Ballester, Julius Rebek, Christopher A. Hunter, Yang Yu
Summary: The study compared the relative contributions of cation-pi interaction and the hydrophobic effect to the binding of molecular guests in synthetic container hosts in water. The results showed that the container molecules preferred binding to the uncharged tert-butyl groups, indicating a stronger interaction compared to cation-pi interactions.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Physical
Haobam Kisan Singh, Upasana Nath, Niharika Keot, Manabendra Sarma
Summary: This article investigates the noncovalent pi-pi interaction and intermolecular electron charge transport involved in host-guest complexes. The study shows that perylene and naphthalene inclusion complexes have the highest and lowest interaction energies, respectively. The conductance values of the complexes increase when the guests are embedded inside the host cavity. The study provides insights into electron transport and offers a direction for the fabrication of future supramolecular molecular devices.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Zheng-Wang Qu, Hui Zhu, Rainer Streubel, Stefan Grimme
Summary: Recently, it has been discovered that dimeric alkylcalcium complexes stabilized by bulky beta-diketiminate ligands can undergo nucleophilic aromatic substitution reactions with benzene upon moderate heating. Extensive calculations show that the strong cation-pi interaction between Lewis acidic calcium centers and the benzene ring plays a crucial role in the cleavage of alkylcalcium dimers, nucleophilic alkyl additions to the benzene ring, and hydride abstraction. Replacing calcium with heavier strontium centers enhances reactivity. This mechanism offers a catalytic approach to nucleophilic aromatic alkylation and H-isotope exchange reactions, potentially solving long-standing issues of multiple alkylation and alkyl isomerization.
Article
Chemistry, Medicinal
Marta Queizan, Marta Sanchez-Lozano, Marcos Mandado, Jose M. Hermida-Ramon
Summary: By combining multiple hydrogen bonds and anion-pi interactions, neutral metal-free receptors are capable of recognizing anions in highly polar solvents. An aromatic molecular tweezer functionalized with azo groups efficiently captures anions in water, exhibiting high thermodynamic stability and strong bonding within the system. Theoretical and first-principles quantum methods confirm the stability of the anion-tweezer complex over time, with the anion consistently located within the cavity of the tweezer.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Correction
Chemistry, Multidisciplinary
P. V. Santhini, V. Jayadev, Sourava C. Pradhan, Sivasankaran Lingamoorthy, P. R. Nitha, M. V. Chaithanya, Rakesh K. Mishra, Narayanan K. N. Unni, Jubi John, Suraj Soman
Summary: The study investigates the application of Indolo[3,2-b]indole donor-based D-pi-A dyes for dye-sensitized solar cells, revealing the crucial role of pi-spacers in recombination processes.
NEW JOURNAL OF CHEMISTRY
(2021)
Article
Chemistry, Inorganic & Nuclear
James R. W. McLay, Joshua J. Sutton, Georgina E. Shillito, Christopher B. Larsen, Gregory S. Huff, Nigel T. Lucas, Keith C. Gordon
Summary: A series of electron donor-acceptor compounds with systematically altered donor and acceptor strengths using different thiophenes and acceptors were investigated in this study. The electronic properties of the compounds were characterized using various spectroscopic techniques and modeled using DFT calculations to study the charge-transfer character of optical transitions. The study found that the electronic absorption spectra were dominated by intraligand charge-transfer transitions, with an increase in charge-transfer character observed across the donor series.
INORGANIC CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Lena Triestram, Fabio Falcioni, Paul L. A. Popelier
Summary: The interaction energies of nine XH center dot center dot center dot pi benzene-containing van der Waals complexes were analyzed using QTAIM multipolar electrostatics and the energy partitioning method IQA/IQF. This study provides a precise understanding of the nature of these interactions, which are important in biochemical systems. The formation of OH center dot center dot center dot pi and NH center dot center dot center dot pi systems is electrostatically driven, while the CH center dot center dot center dot pi interaction has a covalent character.
Article
Chemistry, Inorganic & Nuclear
Javier Pitarch-Jarque, Ramon J. Zaragoza, Rafael Ballesteros, Belen Abarca, Enrique Garcia-Espana, Begona Verdejo, Rafael Ballesteros-Garrido
Summary: By transforming neutral heterocycles into their corresponding salts, new water-soluble fluorescent dyes have been successfully prepared, overcoming the issue of low solubility and helping to reveal the nature of anion-pi interactions in water.
DALTON TRANSACTIONS
(2021)
Article
Chemistry, Physical
Bingwen Long, Jiapo Song, Keke Yao, Yigang Ding
Summary: New density and vapor-liquid equilibrium data of the PCl3-benzene binary system at atmospheric pressure were carefully measured, yielding consistent results through various models and revealing unique interactions and low relative volatility.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Chemistry, Physical
Camilo Zuluaga, Vincent A. Spata, Spiridoula Matsika
Summary: This study compares how 40 different quantum mechanical methods describe the excited states of a guanine-thymine pi-stacked nucleobase dimer system, including both the 5'-TG-3' and 5'-GT-3' conformations. The distance between the nucleobases is found to be a major factor in determining the energy of the CT state and the difference in dipole moments between the CT and ground state. Compared to states localized on one nucleobase, there is a wider range of values (and errors) for the energies of CT states.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
Steve Scheiner
Summary: Sigma-hole bonds and pi-hole bonds rely on the asymmetric distribution of electron density to create a positive region of electrostatic potential for bond formation. Pi-hole bonds established by linear molecules tend to be weaker than those of comparable planar systems.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Biochemistry & Molecular Biology
Qiang Zhao
Summary: The regium-pi stacking interactions in the Au-6⋯PhX complexes were studied, and it was found that the effects of electron-donating and electron-withdrawing substituents on the interactions are different. Moreover, the interactions between substituted benzene and Au-6 cluster were found to be stronger compared to the Au-6⋯benzene complex.
JOURNAL OF MOLECULAR MODELING
(2021)
Article
Biochemistry & Molecular Biology
Asem Alenaizan, Joshua L. Barnett, Nicholas Hud, C. David Sherrill, Anton S. Petrov
Summary: The helical structures of DNA and RNA were revealed through experimental data, and the modeling programs were guided by known structures. Alternative backbone Xeno nucleic acids (XNAs) with different properties can be computationally modeled to search for plausible analogs.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Physical
Jeffrey B. Schriber, Daniel R. Nascimento, Alexios Koutsoukas, Steven A. Spronk, Daniel L. Cheney, C. David Sherrill
Summary: CLIFF is a machine-learned intermolecular force field that combines accurate physics equations with automatic parameterization, achieving high precision in drug discovery and protein models. It demonstrates excellent performance in both test sets and applications by accurately ranking ligand binding strengths and producing low errors compared to reference values.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Asem Alenaizan, Carlos H. Borca, Suneesh C. Karunakaran, Amy K. Kendall, Gerald Stubbs, Gary B. Schuster, C. David Sherrill, Nicholas Hud
Summary: Equimolar mixtures of TAP and CyCo6 self-assemble into gel-forming supramolecular polymers with unique molecular structures. The polymers exhibit different helical structures, suggesting a potential role as recognition units for nucleic acids before the emergence of RNA.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
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)
Editorial Material
Chemistry, Physical
C. David Sherrill, David E. Manolopoulos, Todd J. Martinez, Michele Ceriotti, Angelos Michaelides
JOURNAL OF CHEMICAL PHYSICS
(2021)
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, 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, 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
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.