Article
Chemistry, Physical
Emily E. Claveau, Eric R. Heller, Jeremy O. Richardson, Evangelos Miliordos
Summary: Selective partial oxidation of methane to methanol has been a challenging chemistry problem. Hydrogen-bonding interactions and other effects with the catalyst are found to slow down the undesired methanol oxidation reaction, leading to increased selectivity towards the desired product.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Maciej Baradyn, Artur Ratkiewicz
Summary: In this study, a Reaction Class Transition State Theory (RC-TST) is used to calculate thermal rate constants for hydrogen abstraction by OOH radical from alkanes in the temperature range of 300-2500 K. The rate constants for a reference reaction are obtained with the Canonical Variational Transition State Theory (CVT) augmented with the Small Curvature Tunneling (SCT) correction. The method provides reliable rate constants with a smaller systematic error compared to high level computations.
FRONTIERS IN CHEMISTRY
(2022)
Article
Computer Science, Interdisciplinary Applications
Rui Ming Zhang, Xuefei Xu, Donald G. Truhlar
Summary: TUMME is a program that assembles and solves master equations for gas-phase chemical kinetics based on chemically significant eigenmodes. It interfaces with Gaussian, Polyrate, and/or MSTor output files to calculate flux coefficients for the master equation. TUMME is written in Python 3 with double precision and can run in serial or parallel, while also offering quadruple and octuple precision in some subtasks in C++.
COMPUTER PHYSICS COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Alexander R. Epstein, Jeremy Demarteau, Brett A. Helms, Kristin A. Persson
Summary: The design of circular polymers is necessary due to the lack of efficient recycling methods for many commodity plastics. Polydiketoenamines (PDKs) stand out for their ability to undergo selective depolymerization in strong acid, allowing monomers to be recovered. The chemistry of the cross-linker, far from the reaction center, has been found to affect the depolymerization rate of PDKs, with a proximal amine in the cross-linker significantly accelerating the process.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Thermodynamics
Qian Zhou, Lihong Wei, Yinbo Yang, Tong Hao, Hui Liu
Summary: This study investigated the effects of different loadings of iron on coal-derived char for the heterogeneous reduction of NO. The catalytic mechanism of Fe was revealed through theoretical calculations. The experimental results showed that the char containing 0.4% FeCl3 exhibited the highest catalytic performance, with an NO reduction rate 18.8% higher than that of demineralized char. The catalytic mechanism of Fe was attributed to the creation of new active sites, reduction of energy barriers, and facilitation of N-N bond formation and N-2 desorption from the char surface.
COMBUSTION AND FLAME
(2023)
Article
Chemistry, Physical
Luis P. Viegas
Summary: Experimental work shows that the rate coefficients of OH-initiated oxidation reactions of FTALs are independent of the size of the CxF2x+1 fluoroalkyl chain. This poses a challenge to the MC-TST/CTSR protocol, as the calculated rate coefficients should not vary significantly with increasing values of x. In this study, the MC-TST/CTSR protocol is applied to the x=2,3 cases and the calculated rate coefficients at 298.15 K are found to be k=(2.4 +/- 1.4) x 10(-12) cm(3) molecule(-1) s(-1), practically coincident with the recommended experimental value of k(exp)= (2.8 +/- 1.4)x10(-12) cm(3) molecule(-1) s(-1). Additionally, we demonstrate that tunneling corrections based on improved semiclassical TST are crucial in obtaining Arrhenius-Kooij curves with correct behavior at lower temperatures.
Article
Chemistry, Physical
Eli Pollak, Salvador Miret-Artes
Summary: In this review, we summarize the recent developments in Kramers' theory of reaction rates. We emphasize the importance of this theory in chemical reactions and discuss the main theoretical formalism based on the generalized Langevin equation and the modern Pollak, Grabert and Hanggi theory. The applications of Kramers' theory in quantum and classical surface diffusion are outlined, and recent applications in various fields such as nanoparticle levitation, microcavity polariton dynamics, and reaction simulation in liquids are presented. The open problems and future challenges of Kramers turnover theory are also discussed.
Article
Multidisciplinary Sciences
Robert A. Van Gorder
Summary: The ‘compressed hydrogen atom’ problem involves solving the Schrodinger equation for a hydrogen atom confined within a box with impenetrable boundary. This study investigates the influence of box structure on the ground state energy of the compressed hydrogen atom by examining various shapes and sizes of the box. The theory developed in this study predicts that the ground state energy increases with the first Dirichlet eigenvalue of the box and decreases with the distance of the nucleus from the boundary. Numerical simulations and variational approximations support this prediction. The study also considers the problem of a shell-confined hydrogen atom and proposes a perturbation theory for the approximation of the ground state energy. The results provide a unified framework for understanding confined, high-pressure hydrogen with applications in crystal lattices and metallic hydrogen.
PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES
(2022)
Article
Chemistry, Physical
Changjiao Shang, Lingling Wang, Yunjian Cao, Xiangrui Yu, Yuanzuo Li, Chaofan Sun, Jingang Cui
Summary: In this study, the substituent effect on the excited-state intramolecular proton transfer (ESIPT) reaction of 1,8-Dihydroxyanthraquinone (DHAQ) was investigated using quantum chemistry methods. The analysis of geometric parameters, infrared spectra, and reduced density gradient scatter plots confirmed the strengthening mechanism of excited-state intramolecular hydrogen bonds (IHBs). The relationship between the strength of dual IHBs and the investigated compounds was established based on the calculated binding energies. The study provides valuable guidance for synthesizing efficient ESIPT-based organic chromophores.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Physical
Saad Yalouz, Emiel Koridon, Bruno Senjean, Benjamin Lasorne, Francesco Buda, Lucas Visscher
Summary: In this paper, we introduce several technical and analytical extensions to enhance the efficiency and accuracy of the state-averaged orbital-optimized variational quantum eigensolver (SA-OO-VQE) algorithm. These extensions include an efficient state-resolution procedure and the estimation of gradients and nonadiabatic couplings, which are crucial for practical applications such as conical intersection search and quantum dynamics simulation.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Computer Science, Interdisciplinary Applications
Victor Churchill, Steve Manns, Zhen Chen, Dongbin Xiu
Summary: Recent research has focused on using deep neural networks (DNNs) for data-driven learning of the evolution of unknown systems, aiming to predict the long-term evolution of these systems. Training a DNN with low generalization error is crucial in this case to minimize the accumulation of error over time. However, due to the randomness in DNN training, particularly in stochastic optimization, there is uncertainty in the resulting prediction, leading to uncertainty in the generalization error. This paper introduces a computational technique that reduces the variance of the generalization error, improving the reliability and consistency of the DNN model's predictions.
JOURNAL OF COMPUTATIONAL PHYSICS
(2023)
Article
Chemistry, Physical
Wenqi Chen, Pengchao Zhang, Donald G. Truhlar, Jingjing Zheng, Xuefei Xu
Summary: A new strategy is proposed to automatically identify and separate torsional vibration modes, effectively distinguishing torsional and nontorsional elements and providing ideal frequencies in normal mode analysis, improving the description of thermodynamic properties and kinetics of complex molecules.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Benjamin Helmich-Paris
Summary: In this work, a one-step second-order converger for state-specific and state-averaged complete active space self-consistent field (CASSCF) wave functions is proposed. The method achieves robust convergence through step restrictions and exponential parameterization. It benefits from efficient integral decomposition techniques and demonstrates competitive runtime performance and convergence reliability.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Parandaman Arathala, Rabi A. Musah
Summary: The gas phase mechanism of the chlorine atom-initiated oxidation of methane sulfonamide has been studied using electronic structure methods and chemical kinetic modeling. A major reaction pathway involving H-atom abstraction from the methyl group of methane sulfonamide was identified. Rate coefficients for all possible reaction paths were calculated, and the atmospheric implications were discussed. The reaction of methane sulfonamide with chlorine atom leads to the formation of greenhouse gases and acidic compounds, which contribute to climate change and secondary organic aerosols and acid rain.
ACS EARTH AND SPACE CHEMISTRY
(2023)
Article
Chemistry, Physical
John Strahan, Adam Antoszewski, Chatipat Lorpaiboon, Bodhi P. Vani, Jonathan Weare, Aaron R. Dinner
Summary: This study introduces a new dynamical approximation method, the dynamical Galerkin approximation, to reduce dependence on lag time selection and provide improved estimators for rates and committors. Simple procedures are also proposed for constructing suitable smoothly varying basis functions from arbitrary molecular features, and these methods are evaluated using a dataset.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
Cheng Zhang, Pragya Verma, Jiaxu Wang, Yiwei Liu, Xiao He, Ying Wang, Donald G. Truhlar, Zhonghua Liu
Summary: Kohn-Sham density functional theory is widely used for electronic structure calculations, and the screened-exchange functionals have improved the accuracy of predictions for solid-state properties. This study assesses the performance of six screened-exchange density functionals compared to local functionals in predicting band gaps and lattice constants. The results show that screened-exchange functionals have smaller errors and outperform local functionals. M06-SX shows the best overall performance, with smaller mean absolute errors and lower root-mean-squared errors for both band gaps and lattice constants.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Yinan Shu, Donald G. Truhlar
Summary: This paper discusses the tendency of a time-evolved reduced density matrix for a subsystem to assume a statistical ensemble of states rather than a coherent combination of pure-state wave functions. It also explores the decoherence phenomenon in molecular processes involving changes in the electronic state and the coordinates of the nuclei. The paper presents the necessary background for understanding decoherence, including the description of pure states and mixed states using the density matrix, as well as the concepts of pointer states and decoherence time. It further discusses the treatment of decoherence in the coherent switching with decay of mixing algorithm and the trajectory surface hopping method for semiclassical calculations of electronically nonadiabatic processes.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Correction
Chemistry, Physical
Wenqi Chen, Pengchao Zhang, Donald G. Truhlar, Jingjing Zheng, Xuefei Xu
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Yinan Shu, Linyao Zhang, Dihua Wu, Xiye Chen, Shaozeng Sun, Donald G. Truhlar
Summary: It is recommended to use the fully adiabatic basis for trajectory surface hopping (TSH) calculations, where the Hamiltonian is diagonal. Traditional TSH methods for simulating intersystem crossing processes require explicit computation of nonadiabatic coupling vectors (NACs) in the molecular-Coulomb-Hamiltonian (MCH) basis, in order to compute the gradient in the fully adiabatic basis. However, this explicit requirement hinders the advantages of overlap-based and curvature-driven algorithms used for efficient TSH calculations. A new computation scheme called the time-derivative-matrix scheme is proposed to circumvent the need for NACs.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Giovanni Li Manni, Ignacio Fdez. Galvan, Ali Alavi, Flavia Aleotti, Francesco Aquilante, Jochen Autschbach, Davide Avagliano, Alberto Baiardi, Jie J. Bao, Stefano Battaglia, Letitia Birnoschi, Alejandro Blanco-Gonzalez, Sergey I. Bokarev, Ria Broer, Roberto Cacciari, Paul B. Calio, Rebecca K. Carlson, Rafael Carvalho Couto, Luis Cerdan, Liviu F. Chibotaru, Nicholas F. Chilton, Jonathan Richard Church, Irene Conti, Sonia Coriani, Juliana Cuellar-Zuquin, Razan E. Daoud, Nike Dattani, Piero Decleva, Coen de Graaf, Mickael G. Delcey, Luca De Vico, Werner Dobrautz, Sijia S. Dong, Rulin Feng, Nicolas Ferre, Michael Filatov (Gulak), Laura Gagliardi, Marco Garavelli, Leticia Gonzalez, Yafu Guan, Meiyuan Guo, Matthew R. Hennefarth, Matthew R. Hermes, Chad E. Hoyer, Miquel Huix-Rotllant, Vishal Kumar Jaiswal, Andy Kaiser, Danil S. Kaliakin, Marjan Khamesian, Daniel S. King, Vladislav Kochetov, Marek Krosnicki, Arpit Arun Kumaar, Ernst D. Larsson, Susi Lehtola, Marie-Bernadette Lepetit, Hans Lischka, Pablo Lopez Rios, Marcus Lundberg, Dongxia Ma, Sebastian Mai, Philipp Marquetand, Isabella C. D. Merritt, Francesco Montorsi, Maximilian Morchen, Artur Nenov, Vu Ha Anh Nguyen, Yoshio Nishimoto, Meagan S. Oakley, Massimo Olivucci, Markus Oppel, Daniele Padula, Riddhish Pandharkar, Quan Manh Phung, Felix Plasser, Gerardo Raggi, Elisa Rebolini, Markus Reiher, Ivan Rivalta, Daniel Roca-Sanjuan, Thies Romig, Arta Anushirwan Safari, Aitor Sanchez-Mansilla, Andrew M. Sand, Igor Schapiro, Thais R. Scott, Javier Segarra-Marti, Francesco Segatta, Dumitru-Claudiu Sergentu, Prachi Sharma, Ron Shepard, Yinan Shu, Jakob K. Staab, Tjerk P. Straatsma, Lasse Kragh Sorensen, Bruno Nunes Cabral Tenorio, Donald G. Truhlar, Liviu Ungur, Morgane Vacher, Valera Veryazov, Torben Arne Voss, Oskar Weser, Dihua Wu, Xuchun Yang, David Yarkony, Chen Zhou, J. Patrick Zobel, Roland Lindh
Summary: This article describes the developments of the open-source OpenMolcas chemistry software environment since spring 2020, focusing on the novel functionalities in the stable branch and interfaces with other packages. These developments cover a wide range of topics in computational chemistry and provide an overview of the chemical phenomena and processes that OpenMolcas can address.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Xiaorui Zhao, Yinan Shu, Linyao Zhang, Xuefei Xu, Donald G. Truhlar
Summary: Mixed quantum-classical nonadiabatic dynamics is widely used for simulating molecular dynamics involving multiple electronic states. Trajectory surface hopping (TSH) and self-consistent potential (SCP) methods are the two main categories of such dynamics algorithms. This work illustrates an example of severe population leaking in TSH, which is caused by frustrated hops and long-time simulations driving the excited-state population towards zero over time. The leaking can be partially alleviated by the fewest switches with time uncertainty (TSH) algorithm, but not completely eliminated.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Farideh Badichi Akher, Yinan Shu, Zoltan Varga, Suman Bhaumik, Donald G. Truhlar
Summary: This article presents a method of adding a new type of activation function to a neural network to enforce low-dimensional constraints. By using this method, the interaction potential can be forced to approach zero when subsystems are too far separated to interact, even without sufficient training data. Additionally, improved potential energy surfaces for the 14 lowest (3)A' states of O-3 are provided, and a more general method called parametrically managed diabatization by deep neural network (PM-DDNN) is introduced to add other low-dimensional or lower-level knowledge to machine-learned potentials.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Physical
Maryam Mansoori Kermani, Donald G. Truhlar
Summary: We discovered that two different basis sets labeled as cc-pVxZ are widely used in calculations on Li compounds. However, these calculations produce different results, causing reproducibility issues. In this study, we examined the discrepancies between these supposedly equivalent basis sets for wave function and density functional calculations of Li clusters. We found deviations as large as 22 millihartrees among the basis sets. The noncanonical choices generally resulted in lower energies. Therefore, it is crucial to specify the version of the basis set used in calculations.
CHEMICAL PHYSICS LETTERS
(2023)
Article
Computer Science, Interdisciplinary Applications
Wenqi Chen, Jingjing Zheng, Junwei Lucas Bao, Donald G. Truhlar, Xuefei Xu
Summary: The MSTor program is a computer program that calculates partition functions and thermodynamic functions of complex gas-phase molecules with multiple torsions. It can use multi-structural approximation with torsional anharmonicity (MS-T) based on either a coupled torsional potential or an uncoupled torsional potential. The program also includes eight utility codes for generating input files and comparison results. The 2023 version of MSTor introduces automatic identification of torsional modes with redundant internal coordinates.
COMPUTER PHYSICS COMMUNICATIONS
(2023)
Article
Chemistry, Physical
Farideh Badichi Akher, Yinan Shu, Zoltan Varga, Donald G. Truhlar
Summary: Dynamics simulations of high-energy O(2)-O collisions are crucial for understanding thermal energy content and heat flux in flows around hypersonic vehicles. Recently, a new diabatization method called parametrically managed diabatization by deep neural network (PM-DDNN) has been developed to efficiently treat collisions involving many coupled electronic states. In this study, the PM-DDNN method was applied to the six lowest-energy potential energy surfaces in the O-3 (5) A′ manifold to perform simultaneous diabatization and fitting, and three dynamic methods were used for calculations. The results showed good agreement among the three methods, and electronically nonadiabatic, electronically inelastic, and dissociative cross sections were calculated for various initial conditions.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Dayou Zhang, Donald G. Truhlar
Summary: We present a hybrid multiconfiguration density coherence functional theory (HMC-DCFT) and optimize a density coherence functional by parametrization against a diverse dataset of 59 bond energies and 60 barrier heights. The results are compared to calculations using CASSCF, CASPT2, six Kohn-Sham and hybrid Kohn-Sham exchange-correlation functionals, and three on-top functionals for pair-density functional theory (PDFT) and hybrid PDFT. The new functional outperforms all the compared methods.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Xiaorui Zhao, Isabella C. D. Merritt, Ruiqing Lei, Yinan Shu, Denis Jacquemin, Linyao Zhang, Xuefei Xu, Morgane Vacher, Donald G. Truhlar
Summary: This work discusses nonadiabatic TSH dynamics algorithms employing the curvature-driven approximation and overlap-based time derivative couplings, and presents test calculations on six photochemical reactions. The results show good agreement between the curvature-driven algorithms and overlap-based algorithms.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Daniel S. King, Donald G. Truhlar, Laura Gagliardi
Summary: The selection of active orbitals for modeling strongly correlated electronic states is challenging and highly dependent on the specific states and molecules of interest. The authors propose a discrete variational selection (DVS) approach to tackle this problem by generating multiple trial wave functions from systematically constructed active spaces and choosing the best one variationally. They apply this approach to a database of small-to-medium-sized molecules and find that it performs well in selecting wave functions based on the energy from multiconfiguration pair-density functional theory.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Multidisciplinary
Bo Long, Yu Xia, Yu-Qiong Zhang, Donald G. Truhlar
Summary: In this study, rate constants for the reaction of sulfur trioxide with two water molecules were calculated. It was found that the SO3 + H2O + H2O reaction mechanism is more important than the SO3 + (H2O)2 mechanism at altitudes between 5 and 50 km, and the rate ratio between the two mechanisms is greater than 20 at altitudes between 10 and 35 km.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Ying Yang, Siriluk Kanchanakungwankul, Suman Bhaumik, Qing Ma, Sol Ahn, Donald G. Truhlar, Joseph T. Hupp
Summary: In this study, a Cu-doped ZIF-8 metal-organic framework was synthesized and activated by heating and dosing with O2, methane, and steam. The framework showed catalytic activity for the oxidation of methane to methanol and formaldehyde. Characterization and analysis techniques were used to understand the mechanism of the catalytic reaction.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)