Article
Chemistry, Physical
Yonghao Gu, Zhenyu Zhu, Xin Xu
Summary: Analytic derivative methods in quantum chemistry are powerful tools for calculating molecular properties and simulating chemical systems. Developments in second-order derivative theory for xDH functionals have shown high-quality results in molecular harmonic and anharmonic vibrational frequency calculations, demonstrating the accuracy of xDH functionals in predicting spectroscopic properties for medium-sized molecules.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Physics, Applied
Huijie Zhao, Ziyang Tian, Tao Wu, Yan Li, Haoyun Wei
Summary: The study demonstrates a 1-kHz, single-shot, dynamic, and sensitive flame temperature measurement using hybrid femtosecond/picosecond vibrational coherent anti-Stokes Raman scattering technology. Superior performance is achieved with a temperature inaccuracy of less than 1% and a precision of about 2% at 1790K, showing the potential for accurate and fast temperature measurement in practical or harsh environments.
APPLIED PHYSICS LETTERS
(2021)
Article
Chemistry, Physical
Asylbek A. A. Zhanserkeev, Emily Y. L. Yang, Ryan P. P. Steele
Summary: Ab initio computersimulations of anharmonicvibrationalspectra provide detailed understanding of molecular and complex vibrational behavior. The generation of mode-coupling potentials is the computational bottleneck in such simulations, which can be addressed using a combination of local-mode representation and multilevel methods. By predicting pairwise couplings at a low level of quantum chemistry and recycling excluded pairs at a low level of theory, accurate vibrational self-consistent field calculations can be achieved. Distance-based truncation of low-level predictions further improves computational efficiency without significant loss of accuracy. This combined approach shows promising results in test cases and has potential for accelerating larger systems and higher-order couplings.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Materials Science, Multidisciplinary
Enda Xiao, Chris A. Marianetti
Summary: The classical phonon Green's function can be precisely measured using molecular dynamics to evaluate the range of validity for self-consistent diagrammatic approaches. In this study, we efficiently and precisely calculate the cubic and quartic phonon interactions of CaF2 using the bundled irreducible derivative approach. We find that the 4-phonon sunset diagram plays an important role in the optical phonon linewidths beyond T = 500 K.
Article
Biochemistry & Molecular Biology
Victor A. Lorenz-Fonfria, Kiyoshi Yagi, Shota Ito, Hideki Kandori
Summary: The study revealed the fundamental vibrational characteristics of the chromophore in bacteriorhodopsin membrane protein and its role in the proton-pumping mechanism of the protein. By investigating vibrational spectra, researchers compared differences between all-trans and 13-cis retinal, and identified the overtone and combination transitions of the retinal's C-C stretching vibrations. The latest research suggests that the intensity of overtone C-C transitions in retinal may be overestimated.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Chemistry, Physical
Edward G. Hohenstein, Oumarou Oumarou, Rachael Al-Saadon, Gian-Luca R. Anselmetti, Maximilian Scheurer, Christian Gogolin, Robert M. Parrish
Summary: We propose a Lagrangian-based approach to evaluate relaxed one- and two-particle reduced density matrices from double factorized Hamiltonians, which improves efficiency in computing nuclear gradient and derivative properties.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Jae Woo Park
Summary: The article presents the formulation and implementation of an analytical gradient algorithm for XMCQDPT2 with the resolvent-fitting approximation by Granovsky, demonstrating its power and accuracy compared to canonical XMCQDPT2 theory. The utility of the algorithm in optimizing molecular configurations, evaluating nuclear gradients with many electronic states, and parallelizing the algorithm using the OpenMP/MPI hybrid approach is also discussed, along with the computational cost and parallel efficiency of the program.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Optics
Marc Jankowski, Carsten Langrock, Boris Desiatov, Marko Loncar, M. M. Fejer
Summary: We propose a new approach to supercontinuum generation and carrier-envelope-offset detection based on saturated second-order nonlinear interactions in dispersion-engineered nanowaveguides. The technique developed here broadens the interacting harmonics by forming stable bifurcations of the pulse envelopes due to an interplay between phase-mismatch and pump depletion. The scaling laws suggest that future realization based on this approach could enable supercontinuum generation with orders of magnitude less energy than current state-of-the-art devices.
Article
Materials Science, Multidisciplinary
Jia-Lin Li, Jun-Fang Wu, Chao Li
Summary: This article demonstrates the nonlinear optical effects based on topological resonators, achieving second-harmonic generation (SHG) through the nonlinear interactions between two different types of topological corner modes. These corner modes possess ultrahigh Q factors and large modal overlap factor, simultaneously satisfying the doubly resonant condition for efficient SHG. These findings extend our understanding of nonlinear interactions between higher-order corner modes in a broader framework and have potential applications in topologically-protected imaging and sensing.
RESULTS IN PHYSICS
(2023)
Article
Acoustics
Hamze Mousavi, Moein Mirzaei, Samira Jalilvand
Summary: This study investigates the vibrational properties of a DNA-like structure using a harmonic Hamiltonian and the Green's function formalism. The DNA sequence is treated as a quasi one-dimensional system with randomly distributed mass-spring pairs in each crystalline unit. The results show that increasing the number of mass-spring pairs in the crystalline structure decreases the influence of randomness on the mechanical behavior of the structure.
JOURNAL OF VIBRATION AND CONTROL
(2023)
Article
Chemistry, Physical
Chih-Kai Lin, Qian-Rui Huang, Michitoshi Hayashi, Jer-Lai Kuo
Summary: The study focused on the vibrational spectra of methylammonium ion in organic-inorganic halide perovskites, showing its sensitive and complex features in the 3 μm region. The simulated results were consistent with experimental observations, aiding in interpretation and analysis of experimental data, expanding the research methodology.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Spectroscopy
Neva Agarwala, Leyla Rohani, Gary Hastings
Summary: There is interest in incorporating substituted 1,4-naphthoquinones (NQs) into the A l binding site in photosystem I (PSI) photosynthetic protein complexes, as it alters the bioenergetics of electron transfer in PSI. Time-resolved FTIR studies have been conducted on PSI complexes with disubstituted NQs, comparing their absorption spectra in solution and through density functional theory (DFT) calculations. The calculated and experimental spectra agree well, aiding in making quantitative band assignments and predictions for time-resolved FTIR difference spectra.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2022)
Article
Engineering, Electrical & Electronic
Rende Zhao, Shangqian Wu, Cun Wang, Hailiang Xu, Xianqiang Jiang, Yansong Wang
Summary: The study focused on the implementation of MSOGI in the discrete-time domain for extracting signals with multiple harmonics. It was found that the discretization method greatly impacts the performance, and a novel method was proposed to enhance both the phase and the quadrature characteristic performance. The new method shows promising results both theoretically and experimentally.
IEEE TRANSACTIONS ON POWER ELECTRONICS
(2021)
Article
Chemistry, Multidisciplinary
Chao Wu, Xingxing Jiang, Lin Lin, Yilei Hu, Tianhui Wu, Zheshuai Lin, Zhipeng Huang, Mark G. Humphrey, Chi Zhang
Summary: The study presents the synthesis of a polar NLO vanadate Cs4V8O22 (CVO) with excellent optical properties and strong second-harmonic generation effects achieved through hydrothermal synthesis.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Nanoscience & Nanotechnology
Ziwei Yu, Shiqi Cao, Yingjie Zhao, Yangwu Guo, Meiqiu Dong, Yue Fu, Jinjin Zhao, Jingrun Yang, Lei Jiang, Yuchen Wu
Summary: In this study, lead-free chiral 2D double perovskites were designed and single-crystalline arrays with regulated geometry, pure orientation, and high crystallinity were prepared using the capillary-bridge confined assembly technique. Compared with polycrystalline thin-film counterparts, the microwire arrays demonstrated linearly polarized second harmonic generation (SHG) and higher SHG conversion efficiency.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Biographical-Item
Chemistry, Physical
Rui Fausto, Karolina Anna Haupa, Malgorzata Biczysko, Gyorgy Tarczay
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Editorial Material
Chemistry, Physical
Vadim Ilyushin, Isabelle Kleiner, Masaaki Baba, Malgorzata Biczysko, Michael Schmitt
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Chemistry, Multidisciplinary
Eric Bremond, Alistar Ottochian, Angel Jose Perez-Jimenez, Ilaria Ciofini, Giovanni Scalmani, Michael J. Frisch, Juan Carlos Sancho-Garcia, Carlo Adamo
Summary: The study investigates the performance of newly introduced range-separated double-hybrid functionals, finding that the improved models show higher accuracy for inter-molecular charge-transfer excitation energies.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2021)
Article
Chemistry, Physical
Mingzhu Sheng, Filippo Silvestrini, Malgorzata Biczysko, Cristina Puzzarini
Summary: The study evaluated the structures, relative stabilities, and vibrational wavenumbers of the two most stable conformers of serine using state-of-the-art composite schemes based on coupled-cluster theory. The results indicated that B2PLYP-D3 and DSDPBEP86 are effective methodologies for structural and spectroscopic studies of medium-sized flexible biomolecules, while CCSD(T)/(CBS +CV)(MP2) provided the best overall agreement with experimental data. The composite scheme entirely based on CCSD(T) calculations (CCSD(T)/CBS+CV) confirmed that serine II is the most stable conformer, even with zero-point vibrational energy corrections.
JOURNAL OF PHYSICAL CHEMISTRY A
(2021)
Article
Chemistry, Physical
Ping Wang, Chong Shu, Hexu Ye, Malgorzata Biczysko
Summary: The research aims at establishing an experimentally validated database for amino acids and polypeptides conformers, with the development of a cost-effective composite scheme for conformational energy evaluation. Hybrid functionals B2-PLYP-D3(BJ) and DSD-PBEP86 perform well for structural and energetic characterization of dipeptide analogues, while CAM-B3LYP-D3(BJ) and omega B97X-D3(BJ) represent promising methods for larger peptide-based systems.
JOURNAL OF PHYSICAL CHEMISTRY A
(2021)
Article
Biochemical Research Methods
Youjia Liu, Malgorzata Biczysko, Nigel W. Moriarty
Summary: Nitroxide radicals are long-lived spin-unpaired electronic states that are highly sensitive to their chemical surroundings. They are widely used as spin labels to study protein structure and dynamics. However, in protein crystallography, nitroxide radicals are unusual molecules and their structural information is often inaccurate.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Article
Astronomy & Astrophysics
Yage Zhao, Majdi Hochlaf, Malgorzata Biczysko
Summary: The increased importance of vibrational fingerprints in the identification of molecular systems is highlighted by upcoming observations in various astrochemical environments. Combination of laboratory experiments and theoretical calculations can provide reliable predictions and accurate assignment of spectral transitions, supporting astrochemistry studies beyond currently available experimental data.
FRONTIERS IN ASTRONOMY AND SPACE SCIENCES
(2021)
Article
Chemistry, Physical
Xing Nie, Yong Yang, Tianlv Xu, Malgorzata Biczysko, Steven Kirk, Samantha Jenkins
Summary: This study investigates the effect of deuterium or tritium isotopes bonded to the alpha carbon of glycine using NG-QTAIM. The stress tensor trajectories reveal a transition from S-character chirality to R-character chirality. This finding contributes to the understanding of the extraterrestrial origins of chirality in simple amino acids.
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
(2022)
Article
Chemistry, Physical
Giordano Mancini, Marco Fuse, Filippo Lipparini, Michele Nottoli, Giovanni Scalmani, Vincenzo Barone
Summary: Multiscale methods combining QM/MM are effective in the investigation of spectroscopic properties in condensed phases. This paper reports the development of a novel workflow based on nonperiodic boundary conditions and specific tweaks for rigid body propagation, which allows for accurate simulations with reduced computational cost.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Prachi Sharma, Andrew J. Jenkins, Giovanni Scalmani, Michael J. Frisch, Donald G. Truhlar, Laura Gagliardi, Xiaosong Li
Summary: A new computational method called X2C-MC-PDFT is proposed to account for both electron correlation and relativistic effects in a computationally inexpensive way. Benchmark studies show that X2C-MC-PDFT significantly improves the results compared to previous methods.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Qin Yang, Josef Kapitan, Petr Bour, Julien Bloino
Summary: Combining Raman scattering and Raman optical activity (ROA) with computer simulations allows for the characterization of chiral molecules' fine structure and physicochemical properties. This study presents an accurate and simple approach based on three-quanta anharmonic perturbative mode, showing the significance of anharmonic Raman and ROA spectroscopies in understanding chiral molecules' vibrations and calibrating computational models.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Nora M. Kreienborg, Qin Yang, Corina H. Pollok, Julien Bloino, Christian Merten
Summary: The inclusion of anharmonicity in vibrational spectral analysis is mainly limited to small molecular systems. This limitation is due to the computational costs associated with larger systems and the lack of clear criteria for the identification of resonances. However, recent advances in vibrational perturbation theory (VPT2) have made it possible to handle resonance problems more transparently. This study demonstrates the importance of experimental benchmarking and highlights the mutual stimulation between experimental techniques and computational models.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Maryam Mansoori Kermani, Hanwei Li, Alistar Ottochian, Orlando Crescenzi, Benjamin G. Janesko, Giovanni Scalmani, Michael J. Frisch, Ilaria Ciofini, Carlo Adamo, Donald G. Truhlar
Summary: Theoretical characterization of reactions of complex molecules requires accurate determination of the relative energies of intermediates and transition states. In this study, the DLPNO-CCSD(T) method was employed to provide benchmark values for Diels-Alder transition states leading to strained pentacyclic adducts. Various wave function and density functional methods were compared for their prediction of absolute and relative barrier heights. The results show that only a few density functionals can satisfactorily predict absolute barrier heights, while relative barrier heights are more accurate. The findings of this study can guide the selection of density functionals for future studies on crowded, strained transition states of large molecules.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Jeremy Bourgalais, Zhongming Jiang, Julien Bloino, Olivier Herbinet, Hans-Heinrich Carstensen, Gustavo A. Garcia, Philippe Arnoux, Luc-Sy Tran, Guillaume Vanhove, Laurent Nahon, Frederique Battin-Leclerc, Majdi Hochlaf
Summary: This study presents a combined theoretical and experimental investigation on the synchrotron-based VUV single photon ionization of gas-phase tBuOOH. The ionization energy of tBuOOH and the appearance energy of important fragment ions were estimated. The results are significant for accurately quantifying tBuOOH in gas-phase oxidation/combustion experiments using advanced mass spectrometry techniques.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Multidisciplinary Sciences
Vincenzo Barone, Silvia Alessandrini, Malgorzata Biczysko, James R. Cheeseman, David C. Clary, Anne B. McCoy, Ryan J. DiRisio, Frank Neese, Mattia Melosso, Cristina Puzzarini
Summary: Spectroscopic techniques are essential for probing molecular systems and investigating their properties and dynamics, but the complexity of interpreting the results is increasing. Computational molecular spectroscopy, born as a branch of quantum chemistry, has evolved into a widely-used tool for predicting spectroscopic properties and features in both experimental and theoretical research.
NATURE REVIEWS METHODS PRIMERS
(2021)