Article
Chemistry, Physical
Benjamin J. Carlson, Michael F. Falcetta, Stephen R. Slimak, Kenneth D. Jordan
Summary: The stabilization method is widely used to characterize temporary anions and systems displaying resonances. By identifying the coupling between discrete and continuum states, complex resonance energies can be extracted from stabilization graphs.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Physical
Haichen Xu, Matteo Baggioli, Tom Keyes
Summary: In contrast to solids and gases, there is still a lack of complete theoretical understanding of the vibrational and thermodynamic properties of liquids. This study revisits the properties of liquids within the soft-potential model and shows that many characteristic properties of liquids can be explained at a qualitative level. It discusses the validity of different expressions proposed in literature for the density of unstable modes and explores the role of negative curvature regions and unstable modes in determining the vibrational density of states (VDOS) in liquids. The study also computes the heat capacity within the soft potential model for liquids and confirms that it decreases with temperature, consistent with experimental and simulation data.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Correction
Engineering, Multidisciplinary
Mehdi Sabzevari
Summary: This review article examines and corrects major scientific errors in the paper by Mirzaee (2014), presenting accurate methods and relevant formulas for replacement. The corrected method is illustrated through numerical examples with results presented.
AIN SHAMS ENGINEERING JOURNAL
(2021)
Article
Computer Science, Software Engineering
Graeme Gange, Zequn Ma, Jorge A. Navas, Peter Schachte, Harald Sondergaard, Peter J. Stuckey
Summary: The article explores the popular abstract domains of Zones and Octagons for static program analysis, presenting fast implementations and comparing their performance against alternative approaches. The experiments demonstrate significant improvements in the state of the art for both Zones and Octagons with the new implementations.
ACM TRANSACTIONS ON PROGRAMMING LANGUAGES AND SYSTEMS
(2021)
Correction
Cell Biology
Mingxu Song, Yuan Yin, Jiwei Zhang, Binbin Zhang, Zehua Bian, Chao Quan, Leyuan Zhou, Yaling Hu, Qifeng Wang, Shujuan Ni, Bojian Fei, Weili Wang, Xiang Du, Dong Hua, Zhaohui Huang
Summary: The display of Fig. 1 in the original publication was incorrect, and the correct figure is available in this correction.
Article
Chemistry, Physical
Josefine H. Andersen, Kaushik D. Nanda, Anna Krylov, Sonia Coriani
Summary: This article discusses several strategies for computing electronic circular dichroism (CD) spectra at the equation-of-motion coupled-cluster singles and doubles level of theory across different frequency ranges. CD spectra of both ground and electronically excited states are considered. The approach is compared with coupled-cluster linear response results and time-dependent density functional theory for selected cases. The extension of the theory to include the effect of spin-orbit coupling is demonstrated by calculations of X-ray CD spectra at the L-edge.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Multidisciplinary
Felix Plasser, Anna Krylov, Andreas Dreuw
Summary: libwfa is an open-source software library for wavefunction analysis, offering a variety of analysis methods for post-processing excited-state calculations. These tools provide graphical representations of various excited-state processes and offer insights into electronic structure. The software is capable of automated processing of large data sets and establishes a link between many-body wavefunctions and physical and chemical models.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2022)
Article
Chemistry, Physical
Goran Giudetti, Igor Polyakov, Bella L. Grigorenko, Shirin Faraji, Alexander V. Nemukhin, Anna I. Krylov
Summary: This work explores the importance of transparency in reporting computational protocols for achieving reproducibility in QM/MM simulations. By simulating a chemical reaction in a biomolecule as a test case, the study shows that reproducing key energy calculations from two software packages is challenging. The results indicate that minor details of the QM/MM simulations need to be reported to ensure reproducibility, and suggestions are provided for developing practical guidelines for reporting biosimulation results.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Multidisciplinary
Saikiran Kotaru, Sven Kahler, Maristella Alessio, Anna Krylov
Summary: The exchange coupling constants for a set of iron (III) binuclear and tetranuclear complexes are calculated using non-collinear spin-flip time-dependent density functional theory (NC-SF-TDDFT). The results show good agreement with experimentally derived values. The applicability of the Heisenberg model is explored by analyzing bonding patterns and natural orbitals (NO). The efficiency of the spin-flip protocol in computing exchange couplings and the utility of NO analysis in assessing the validity of effective spin Hamiltonians are demonstrated.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Florian Matz, Thomas-Christian Jagau
Summary: Auger decay is a relaxation process in atoms and molecules, which can be described using complex-variable coupled-cluster (CC) methods. Channel-specific core-valence projectors, called Auger channel projectors, are introduced to evaluate partial widths. The combination of CIS calculations based on different reference states can effectively recover the decay widths of Auger decay.
Article
Chemistry, Physical
Pawel Wojcik, Eric R. Hudson, Anna Krylov
Summary: This study systematically investigates the diatomic radical-cations composed of a metal and a ligand, and finds that the electronic transitions in these cations for optical cycling are less effective compared to the successfully laser-cooled neutral molecules. Alternative transitions suitable for optical cycling are proposed, providing insights for the design of OCCs in charged or neutral molecules.
Article
Chemistry, Physical
Madhubani Mukherjee, T. P. Ragesh Kumar, Milos Rankovic, Pamir Nag, Juraj Fedor, Anna I. Krylov
Summary: We present a study that combines experimental and theoretical methods to investigate the interaction between electrons and molecules using pyrrole as a model system. The experimental two-dimensional electron energy loss spectra (EELS) provide information about the molecular vibrational states and electronic resonances. The calculations using complex-valued extensions of equation-of-motion coupled-cluster theory help identify the major EELS features. The results confirm previously described pi resonances and predict a low-lying resonance with a mixed character, providing insights into the vibrational excitation patterns observed in the EELS.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Kaushik D. D. Nanda, Sahil Gulania, Anna I. I. Krylov
Summary: The equation-of-motion coupled-cluster singles and doubles method with double electron attachment (EOM-DEA-CCSD) is extended to calculate two-photon absorption (2PA) cross sections of diradicals and polyenes. The performance of this new implementation is compared with the CC3 quadratic response theory approach. The EOM-DEA-CCSD 2PA cross sections are comparable to the CC3 results for twisted ethene, but show large discrepancies for hexatriene, explained by configurational analysis of the 2PA channels.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Nayanthara K. Jayadev, Anthuan Ferino-Perez, Florian Matz, Anna I. Krylov, Jagau Thomas-C.
Summary: We conducted an ab initio computational study on the Auger electron spectrum of benzene. Using coupled-cluster theory and equation-of-motion coupled-cluster theory, we described the decaying nature of core-ionized states through two approaches and found that the computed spectra from both approaches agreed well with experimental Auger spectra. The Auger spectrum of benzene exhibits well-resolved peaks above 260 eV corresponding to final states with electrons removed from the highest occupied molecular orbitals.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Michael Epshtein, Bruno Nunes Cabral Tenorio, Marta L. Vidal, Valeriu Scutelnic, Zheyue Yang, Tian Xue, Anna I. Krylov, Sonia Coriani, Stephen R. Leone
Summary: Tabletop X-ray spectroscopy measurements and ab initio calculations are used to investigate the influence of the bromine atom on carbon core-valence transitions in the bromobenzene cation. The results show that replacing a hydrogen atom with a bromine atom in benzene shifts the transition energy in the X-ray spectrum. Moreover, the X-ray spectrum of the bromobenzene cation is dominated by two intense transitions, which are enhanced compared to the neutral bromobenzene.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Physical
Ronit Sarangi, Kaushik D. Nanda, Anna I. Krylov
Summary: This computational study investigates the charge-transfer-to-solvent (CTTS) states of aqueous thiocyanate anion using equation-of-motion coupled-cluster methods and electrostatic embedding QM/MM scheme. The results from classical molecular dynamics (MD) and QM/MM ab initio molecular dynamics (AIMD) simulations show significant differences in the local structure around solvated SCN-. The sensitivity of the CTTS states to the solvent structure suggests that CTTS-based spectroscopy can be used to assess the quality of force-fields and density functionals. By combining CTTS-based spectroscopy with theoretical modeling, detailed microscopic information of the solvent structure can be obtained.
Article
Chemistry, Physical
Axel Molle, Oleg Zatsarinny, Thomas Jagau, Alain Dubois, Nicolas Sisourat
Summary: Researchers have found that interatomic Coulombic electron capture, a process that attaches electrons to atoms, can be achieved through energy transfer to nearby neighbors. This electron capture process is more powerful than environment-independent photorecombination when the electron energy exceeds a certain threshold. The findings have significant implications for the study of low-energy electrons, particularly in understanding radiation-induced damage to biomolecules.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Florian Matz, Jonas Nijssen, Thomas-C. Jagau
Summary: In this study, we investigate the Auger spectra of methane, ethane, ethylene, and acetylene using ab initio computational methods. Auger spectroscopy, a technique to probe the electronic structure of molecules, is based on the Auger-Meitner effect of core-ionized states. We calculate partial decay widths using coupled-cluster theory (CCSD) and equation-of-motion CCSD theory combined with complex-scaled basis functions and Feshbach-Fano projection. From these partial widths, we generate Auger spectra and draw conclusions about specific decay channels and trends among the four molecules. We also establish a connection to experimental results on the fragmentation pathways of electronic states produced by Auger decay.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Physical
Joel Creutzberg, Wojciech Skomorowski, Thomas-C. Jagau
Summary: In this study, we compute the autoionization widths of various Rydberg states of neon and N2 using equation-of-motion coupled-cluster theory combined with complex scaling and complex basis functions. This study represents the first application of complex-variable methods to Rydberg states represented in Gaussian basis sets. A new computational protocol based on Kaufmann basis functions is designed to make these methods applicable to atomic and molecular Rydberg states. The results demonstrate a decrease in the decay width with increasing angular momentum and principal quantum number within both Rydberg series.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
