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
Astronomy & Astrophysics
Xiong-Hui Cao, Qu-Zhi Li, Zhi-Hu Guo, Han-Qing Zheng
Summary: In this study, an extended Roy equation is used to investigate ππ scatterings at unphysical large pion masses, where σ becomes a bound state in one situation and remains a broad resonance in another case. The coupled integral equations at large pion masses are solved by considering lattice driving terms and Regge amplitudes as inputs. Using the solutions of Roy equations that satisfy unitarity, analyticity, and crossing symmetry, we make predictions for the phase shifts with IJ = 00, 11, and 20 in the elastic energy region. We then analytically continue into the complex s plane to search for various poles, all of which lie within the valid domain of the Roy equation. This is the first time that lattice data at unphysical large pion masses are analyzed using the rigorous Roy equation method.
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
Astronomy & Astrophysics
Y. Unal, D. Severt, J. de Vries, C. Hanhart, Ulf-G Meissner
Summary: Triggered by experimental prospects, this study calculates the CP-odd electric dipole moments (EDMs) of spin-1/2 single-bottom baryons and discusses the expected size of the EDMs for beyond-the-Standard-Model physics appearing at the TeV scale.
Article
Chemistry, Physical
Ren A. Wiscons, Rahul Nikhar, Krzysztof Szalewicz, Adam J. Matzger
Summary: This study compares hydrates and hydrogen peroxide solvates in terms of their structure, interaction, and impact on the performance of drugs and explosives. By analyzing crystal structures and potential energy surfaces, the research provides a foundation for designing and selecting candidate molecules for hydrogen peroxide solvates.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
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
Astronomy & Astrophysics
Hao Liu, Yuan-He Zou, Yan-Rui Liu, Shao-Zhou Jiang
Summary: The relativistic chiral Lagrangians for doubly charmed baryons of spin-1/2 and spin-3/2 are constructed up to the order O(p(4)). There are a total of 19, 74, and 452 independent terms in the two-flavor case and 25, 112, and 864 independent terms in the three-flavor case from O(p(2)) to O(p(4)). The chiral Lagrangians in the heavy diquark limit are also obtained.
Article
Computer Science, Interdisciplinary Applications
A. Mercenne, K. D. Launey, T. Dytrych, J. E. Escher, S. Quaglioni, G. H. Sargsyan, D. Langr, J. P. Draayer
Summary: We study the effectiveness of a new ab initio framework that combines the symmetry-adapted nocore shell-model approach with the resonating group method for unified descriptions of nuclear structure and reactions. Ab initio neutron-nucleus interactions are obtained for 4He, 16O, and 20Ne targets. The study demonstrates the efficacy of the proposed framework and its scalability with particle numbers and model space dimensions, with the aim of ab initio descriptions of nucleon scattering and capture reactions in the medium-mass region.
COMPUTER PHYSICS COMMUNICATIONS
(2022)
Article
Physics, Particles & Fields
Yasser Akou, Mohammad R. Garousi
Summary: In this paper, the classical effective action of the O-plane and its corresponding boundary terms in type II superstring theories at order alpha ' 2 and for NS-NS couplings are investigated using constraints of gauge transformations and string duality transformations. It is found that these constraints fix the bulk action and its corresponding boundary terms up to one overall factor, while also producing three multiplets in the boundary action with coefficients independent of the bulk couplings under string dualities.
EUROPEAN PHYSICAL JOURNAL C
(2021)
Article
Computer Science, Interdisciplinary Applications
P. Arthuis, A. Tichai, J. Ripoche, T. Duguet
Summary: The second version of the code ADG automates the generation and evaluation of valid off-diagonal Bogoliubov many-body perturbation theory diagrams. It can handle Hamiltonians with both two-body and three-body interactions, and utilizes algebraic Feynman's rules and diagrammatic rules for evaluation. The program has been optimized for efficiency and moved to Python3, while still supporting Python2.
COMPUTER PHYSICS COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Marco Caricato, Ty Balduf
Summary: The study introduces a new method for computing the optical rotation tensor, which is simpler and less computationally demanding compared to other methods. Comparison of results on 22 organic molecules shows a good linear correlation between the LG(OI) and MVG approaches.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Materials Science, Multidisciplinary
Yong-Yi Huang
Summary: This paper explains that the canonical transformations in matrix mechanics are actually just transformations of different representations in standard quantum mechanics. It also demonstrates the non-degenerate, degenerate, and time-dependent perturbation theory in matrix mechanics, solving the mystery of time-dependent perturbation theory in this context. Additionally, the Kramers' dispersion formula from time-dependent perturbation theory in matrix mechanics is derived from wave mechanics.
RESULTS IN PHYSICS
(2022)
Article
Astronomy & Astrophysics
Vanamali Shastry, Enrico Trotti, Francesco Giacosa
Summary: By using the covariant helicity formalism, we study the two-body decays of mesons and constrain the interacting terms in the Lagrangian. Utilizing partial wave analysis, we make predictions for unmeasured quantities and investigate the isoscalar mixing angle in various mesonic sectors, with results matching those from LHCb and confirming significant contributions from the axial anomaly.
Review
Chemistry, Multidisciplinary
Alex Elmi, Scott L. Cockroft
Summary: Supramolecular chemistry focuses on interactions between molecules, while molecular chemistry is centered on bonds within molecules. Understanding molecular self-assembly processes remains a challenge, particularly due to computational and practical limitations regarding solvation effects. Tackling these challenges requires a combination of experimental and computational approaches to study the role of solvents in molecular recognition.
ACCOUNTS OF CHEMICAL RESEARCH
(2021)
Article
Chemistry, Physical
Aliakbar Sepehri, Run R. Li, Mark R. Hoffmann
Summary: The importance of localized molecular orbitals (MOs) in correlation treatments beyond mean-field calculation and in the illustration of chemical bonding is discussed. A method for obtaining orthonormal localized virtual MOs is introduced. The method allows the use of highly efficient group theoretical methods for calculation of Hamiltonian matrix elements and provides qualitative understanding of bonding in molecules.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Medicinal
Kristian Kriz, Jan Rezac
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2019)
Article
Chemistry, Multidisciplinary
Jan Rezac
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2019)
Article
Chemistry, Medicinal
Kristian Kriz, Jan Rezac
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2020)
Article
Chemistry, Physical
B. Hourahine, B. Aradi, V. Blum, F. Bonafe, A. Buccheri, C. Camacho, C. Cevallos, M. Y. Deshaye, T. Dumitrica, A. Dominguez, S. Ehlert, M. Elstner, T. van der Heide, J. Hermann, S. Irle, J. J. Kranz, C. Koehler, T. Kowalczyk, T. Kubar, I. S. Lee, V. Lutsker, R. J. Maurer, S. K. Min, I. Mitchell, C. Negre, T. A. Niehaus, A. M. N. Niklasson, A. J. Page, A. Pecchia, G. Penazzi, M. P. Persson, J. Rezac, C. G. Sanchez, M. Sternberg, M. Stoehr, F. Stuckenberg, A. Tkatchenko, V. W. -z. Yu, T. Frauenheim
JOURNAL OF CHEMICAL PHYSICS
(2020)
Article
Chemistry, Physical
Jan Rezac
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2020)
Review
Chemistry, Multidisciplinary
Adam Pecina, Saltuk M. Eyrilmez, Cemal Kopruluoglu, Vijay Madhav Miriyala, Martin Lepsik, Jindrich Fanfrlik, Jan Rezac, Pavel Hobza
Article
Chemistry, Physical
Jan Rezac
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2020)
Editorial Material
Chemistry, Multidisciplinary
Adam Pecina, Saltuk M. Eyrilmez, Cemal Koepruelueoglu, Vijay Madhav Miriyala, Martin Lepsik, Jindrich Fanfrlik, Jan Rezac, Pavel Hobza
Article
Chemistry, Physical
Kristian Kriz, Martin Novacek, Jan Rezac
Summary: The study investigates repulsive contacts in molecular complexes and emphasizes the importance of repulsive part in computational methods. The results show that double-hybrid functionals perform the best, while GFN2-xTB stands out among semiempirical methods. By analyzing the source of error, the study successfully corrects the most serious uncorrected issues encountered in practical calculations.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
Chandler Greenwell, Jan Rezac, Gregory J. O. Beran
Summary: A spin-component-scaled, dispersion-corrected MP2 model (SCS-MP2D) is proposed to address the limitations of MP2 in describing dispersion interactions and reaction thermochemistry. Experimental results show that SCS-MP2D considerably improves the accuracy of MP2 and is comparable in accuracy and computational cost to state-of-the-art density functionals.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
J. Rezac, J. J. P. Stewart
Summary: Semiempirical quantum-mechanical computational methods are widely used in the study of biomolecular systems, but their ability to accurately describe protein structures is not well understood. In this study, the structures of 19 proteins were optimized using several semiempirical QM methods, and compared to high-resolution crystal structures. Some methods showed good agreement with the experimental structures, while others introduced artificial close contacts that could be improved through reparameterization.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Kristian Kriz, Jan Rezac
Summary: The SH250x10 dataset extends the Non-Covalent Interactions Atlas database to complexes bound by sigma-hole interactions and is used for testing various DFT functionals and semiempirical quantum-mechanical methods.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Jan Rezac
Summary: The Non-Covalent Interactions Atlas has expanded with two data sets to study benchmark interaction energies in complexes dominated by London dispersion. These high-quality data sets enable comprehensive testing of various non-covalent interactions in a wide range of chemical space.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Ondrej Gutten, Petr Jurecka, Zahra Aliakbar Tehrani, Milos Budesinsky, Jan Rezac, Lubomir Rulisek
Summary: The performance of computational methods in modeling cyclic dinucleotides has been evaluated through two benchmarks, showing that most density functional approximations are accurate enough, but struggle in reproducing the conformation of purine bases. The overrepresentation of syn-conformation of guanine in PC1 indicates the need for improvement in implicit solvation models and force-field parameters.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Jindrich Fanfrlik, Adam Pecina, Jan Rezac, Martin Lepsik, Menyhart B. Sarosi, Drahomir Hnyk, Pavel Hobza