Article
Chemistry, Physical
Jiaxin Chen, Chengyuan Zhang, Yanling Lu, Hainan Wang, Yongqing Li
Summary: A large number of ab initio energy points were calculated using the aug-cc-pV(Q,5)Z basis sets and extrapolated to the complete basis set limit. An exact potential energy surface of the ground-state BH2+ was obtained, and a switching function was developed to model transitions. The topographic features of the new global potential energy surface were discussed in detail, and integral cross sections of a reaction were calculated using the quasi-classical trajectory method.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Article
Chemistry, Physical
Ignacio Ema, Guillermo Ramirez, Rafael Lopez, Jesus San Fabian, Jose M. Garcia de la Vega
Summary: This study investigates weakly bound neon dimer, trimer and tetramers using various basis sets. The study examines their binding energies and structural properties. The results show that the SIGMA-s basis sets perform well in this study and can be applied to the study of larger weakly bound systems of other atoms. Difficulties in obtaining accurate results are assessed through computations of total, atomization, and correlation energies, as well as equilibrium distances using different basis sets of increasing size. Extrapolations are proposed to predict stabilization energies and compared with previously published data.
Article
Chemistry, Physical
Vijay Gopal Chilkuri, Frank Neese
Summary: This work focuses on benchmark calculations based on the ICE program and compares the performance of different types of many-particle basis functions. By analyzing the number of wavefunction parameters, energy error, and the best way to extrapolate ICE energies towards FCI results, the study explores the implications of the three many-particle representations in selected CI implementations.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Multidisciplinary
Yonggang Jiang, Dongxiang Liu, Madeline E. Rotella, Guogang Deng, Zhengfen Liu, Wen Chen, Hongbin Zhang, Marisa C. Kozlowski, Patrick J. Walsh, Xiaodong Yang
Summary: In this article, the first amidyl radicals were reported to preferentially undergo a net 1,2-HAT over 1,5-HAT. The amidyl radicals were generated by single electron transfer from 2-azaallyl anions to N-alkyl N-aryloxy amides. The amidyl radicals then underwent net 1,2-HAT to generate C-centered radicals.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
R. Aravindhan, Jianping Hu, M. Ummal Momeen
Summary: The polarity of solvents has a significant impact on the optical absorption and electronic structure of 1-iodoadamantane, resulting in solvatochromic shifts. The absorption shift for sigma to sigma* and n to sigma* electronic transitions is more pronounced in polar solvents.
Article
Chemistry, Physical
Michael Glasbrenner, Sigurd Vogler, Christian Ochsenfeld
Summary: A method using second-order Moller-Plesset perturbation theory for computing NMR shieldings efficiently derives equations from Laplace-transformed atomic orbitals, minimizing the number of equations to be solved with the Z-vector approach. The method also utilizes the resolution-of-the-identity approximation and Cholesky decomposition of pseudo-density matrices, as well as exploiting sparsity in three-center integrals with sparse linear algebra approaches. Test calculations show small deviations from NMR shifts obtained with canonical MP2, and the method's performance is illustrated in calculations on DNA strands and glycine chains.
JOURNAL OF CHEMICAL PHYSICS
(2021)
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
Chemistry, Physical
Frank Jensen
Summary: We investigated three different methods for extrapolating harmonic vibrational frequencies to the complete basis set limit: direct extrapolation of frequencies, calculation of frequencies based on extrapolated Hessians, or based on the Hessian from optimization of the extrapolated energy surface. For regular molecules, all three methods yielded similar results, but for loosely bound complexes, frequencies derived from extrapolated Hessians showed unpredictable behavior. However, none of the basis set extrapolations significantly improved upon the results used for extrapolation.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Multidisciplinary
Juan C. Zapata Trujillo, Laura K. McKemmish
Summary: Harmonic frequency calculations often overestimate experimental frequencies, requiring multiplicative scaling factors. Analysis of 1495 scaling factors shows convergence and domination of anharmonicity error with hybrid functionals and double-zeta basis sets. Persistent minimum error of 25 cm(-1) highlights the need for accurate treatment of anharmonicity in model chemistry choices.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2022)
Article
Chemistry, Physical
Enrique M. Cabaleiro-Lago, Berta Fernandez, Roberto Rodriguez-Fernandez, Jesus Rodriguez-Otero, Saulo A. Vazquez
Summary: Analytical corrections were developed to improve the accuracy of the PM6 and GFN2-xTB semiempirical quantum mechanical methods for evaluating noncovalent interaction energies in alkanes and alkenes. The approach of functional group corrections was used, where the atom-atom pair corrections depend on the nature of the interacting functional groups. The results showed that the errors obtained with the PM6-FGC and xTB-FGC methods for the included systems were within the chemical accuracy.
JOURNAL OF CHEMICAL PHYSICS
(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
Janine Hellmers, Carolin Koenig
Summary: A flexible formulation for energy-based molecular fragmentation schemes has been introduced, which can incorporate existing and novel fragmentation expansions. The application of this framework in multi-level approaches and electronic interaction energies has been illustrated, showing its ability to generate well-suited multi-level fragmentation expansions for different cases. The study successfully reproduces electronic protein-protein interaction energies with high accuracy for various structures.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Jiachen Li, Ye Jin, Neil Qiang Su, Weitao Yang
Summary: The localized orbital scaling correction (LOSC) applied in the Bethe-Salpeter equation (BSE) accurately predicts excitation energies for molecules, eliminating delocalization errors and approximating quasiparticle (QP) energies with accuracy comparable to or better than the GW Green's function approach, and at a much lower computational cost. The BSE/LOSC approach outperforms commonly used methods for predicting excitations with different characters, showing promise as an efficient method for calculating excitation energies in molecular systems.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Tom Speelman, Ana Cunha, R. K. Kathir, Remco W. A. Havenith
Summary: The study proposes a modification to the calculation of effective electronic coupling and suggests that the aug-cc-pVDZ and 6-311++G** basis sets are a good compromise between accuracy and computational feasibility for future research on larger clusters of molecules.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2021)
Article
Chemistry, Medicinal
Donghan Wang, Wenze Li, Xu Dong, Hongzhi Li, LiHong Hu
Summary: This study proposes an interpretable noncovalent interaction (NCI) prediction model called TFRegNCI, based on RegNet feature extraction and a transformer encoder fusion strategy. The model achieves high accuracy and efficiency by using a transformer encoder for feature fusion and 2D inputs instead of 3D inputs. The addition of the visualization module, Grad-RAM, enhances the interpretability of the model by displaying feature maps and validating their significance.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(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