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Mendolicchio M, Barone V. Accurate Vibrational and Ro-Vibrational Contributions to the Properties of Large Molecules by a New Engine Employing Curvilinear Internal Coordinates and Vibrational Perturbation Theory to Second Order. J Chem Theory Comput 2024. [PMID: 39215708 DOI: 10.1021/acs.jctc.4c00857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
The unbiased comparison between theory and experiment requires approaches more sophisticated than the basic harmonic-oscillator rigid-rotor model, for taking into account vibrational averaging effects and ro-vibrational couplings in molecules of increasing size. Second-order vibrational perturbation theory based on curvilinear internal coordinates (ICs) offers a remarkable compromise between accuracy and computational cost, thanks to the reduction of mode-mode couplings with respect to their counterparts based on Cartesian coordinates. Therefore, we have developed, implemented, and validated a general engine employing ICs, which allows the accurate evaluation of vibrational averages and ro-vibrational couplings for molecules containing up to about 50 atoms beyond the harmonic approximation. After validation of the new tool for relatively small molecules, the effectiveness of ICs has been demonstrated for some flexible and/or quite large molecular bricks of life.
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2
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Xu Y, Liu C, Ma H. Kylin-V: An open-source package calculating the dynamic and spectroscopic properties of large systems. J Chem Phys 2024; 161:052501. [PMID: 39087896 DOI: 10.1063/5.0220712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 07/14/2024] [Indexed: 08/02/2024] Open
Abstract
Quantum dynamics simulation and computational spectroscopy serve as indispensable tools for the theoretical understanding of various fundamental physical and chemical processes, ranging from charge transfer to photochemical reactions. When simulating realistic systems, the primary challenge stems from the overwhelming number of degrees of freedom and the pronounced many-body correlations. Here, we present Kylin-V, an innovative quantum dynamics package designed for accurate and efficient simulations of dynamics and spectroscopic properties of vibronic Hamiltonians for molecular systems and their aggregates. Kylin-V supports various quantum dynamics and computational spectroscopy methods, such as time-dependent density matrix renormalization group and our recently proposed single-site and hierarchical mapping approaches, as well as vibrational heat-bath configuration interaction. In this paper, we introduce the methodologies implemented in Kylin-V and illustrate their performances through a diverse collection of numerical examples.
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Affiliation(s)
- Yihe Xu
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Chungen Liu
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Haibo Ma
- Qingdao Institute for Theoretical and Computational Sciences, School of Chemistry and Chemical Engineering, Shandong University, Qingdao 266237, China
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3
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Spencer RJ, Zhanserkeev AA, Yang EL, Steele RP. The Near-Sightedness of Many-Body Interactions in Anharmonic Vibrational Couplings. J Am Chem Soc 2024; 146:15376-15392. [PMID: 38771156 DOI: 10.1021/jacs.4c03198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Couplings between vibrational motions are driven by electronic interactions, and these couplings carry special significance in vibrational energy transfer, multidimensional spectroscopy experiments, and simulations of vibrational spectra. In this investigation, the many-body contributions to these couplings are analyzed computationally in the context of clathrate-like alkali metal cation hydrates, including Cs+(H2O)20, Rb+(H2O)20, and K+(H2O)20, using both analytic and quantum-chemistry potential energy surfaces. Although the harmonic spectra and one-dimensional anharmonic spectra depend strongly on these many-body interactions, the mode-pair couplings were, perhaps surprisingly, found to be dominated by one-body effects, even in cases of couplings to low-frequency modes that involved the motion of multiple water molecules. The origin of this effect was traced mainly to geometric distortion within water monomers and cancellation of many-body effects in differential couplings, and the effect was also shown to be agnostic to the identity of the ion. These outcomes provide new understanding of vibrational couplings and suggest the possibility of improved computational methods for the simulation of infrared and Raman spectra.
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Affiliation(s)
- Ryan J Spencer
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Asylbek A Zhanserkeev
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Emily L Yang
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Ryan P Steele
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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4
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Mendolicchio M, Barone V. Unbiased Comparison between Theoretical and Experimental Molecular Structures and Properties: Toward an Accurate Reduced-Cost Evaluation of Vibrational Contributions. J Chem Theory Comput 2024; 20:2842-2857. [PMID: 38556752 DOI: 10.1021/acs.jctc.4c00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
The tremendous development of hardware and software is constantly increasing the role of quantum chemical (QC) computations in the assignment and interpretation of experimental results. However, an unbiased comparison between theory and experiment requires the proper account of vibrational averaging effects. In particular, high-resolution spectra in the gas phase are now available for molecules containing up to about 50 atoms, which are too large for a brute-force approach with the available QC methods of sufficient accuracy. In the present paper, we introduce hybrid approaches, which allow the accurate evaluation of vibrational averaging effects for molecules of this size beyond the harmonic approximation, with special attention being devoted to rotational constants. After the validation of new tools for relatively small molecules, the β-estradiol hormone and a prototypical molecular motor have been considered to witness the feasibility of accurate computations for large molecules.
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5
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Uribe L, Di Grande S, Crisci L, Lazzari F, Mendolicchio M, Barone V. Accurate Structures and Rotational Constants of Steroid Hormones at DFT Cost: Androsterone, Testosterone, Estrone, β-Estradiol, and Estriol. J Phys Chem A 2024; 128:2629-2642. [PMID: 38530336 DOI: 10.1021/acs.jpca.4c00573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
A comprehensive analysis of the structural, conformational, and spectroscopic properties in the gas phase has been performed for five prototypical steroid hormones, namely, androsterone, testosterone, estrone, β-estradiol, and estriol. The revDSD-PBEP86 double-hybrid functional in conjunction with the D3BJ empirical dispersion and a suitable triple-ζ basis set provides accurate conformational energies and equilibrium molecular structures, with the latter being further improved by proper account of core-valence correlation. Average deviations within 0.1% between computed and experimental ground state rotational constants are reached when adding to those equilibrium values vibrational corrections obtained at the cost of standard harmonic frequencies thanks to the use of a new computational tool. Together with the intrinsic interest of the studied hormones, the accuracy of the results obtained at DFT cost for molecules containing about 50 atoms paves the way toward the accurate investigations of other flexible bricks of life.
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Affiliation(s)
- Lina Uribe
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Scuola Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
| | - Silvia Di Grande
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Scuola Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
| | - Luigi Crisci
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Federico Lazzari
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Marco Mendolicchio
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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6
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Streu K, Hunsberger S, Patel J, Wan X, Daly CA. Development of a universal method for vibrational analysis of the terminal alkyne C≡C stretch. J Chem Phys 2024; 160:074106. [PMID: 38364010 DOI: 10.1063/5.0185580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/07/2024] [Indexed: 02/18/2024] Open
Abstract
The terminal alkyne C≡C stretch has a large Raman scattering cross section in the "silent" region for biomolecules. This has led to many Raman tag and probe studies using this moiety to study biomolecular systems. A computational investigation of these systems is vital to aid in the interpretation of these results. In this work, we develop a method for computing terminal alkyne vibrational frequencies and isotropic transition polarizabilities that can easily and accurately be applied to any terminal alkyne molecule. We apply the discrete variable representation method to a localized version of the C≡C stretch normal mode. The errors of (1) vibrational localization to the terminal alkyne moiety, (2) anharmonic normal mode isolation, and (3) discretization of the Born-Oppenheimer potential energy surface are quantified and found to be generally small and cancel each other. This results in a method with low error compared to other anharmonic vibrational methods like second-order vibrational perturbation theory and to experiments. Several density functionals are tested using the method, and TPSS-D3, an inexpensive nonempirical density functional with dispersion corrections, is found to perform surprisingly well. Diffuse basis functions are found to be important for the accuracy of computed frequencies. Finally, the computation of vibrational properties like isotropic transition polarizabilities and the universality of the localized normal mode for terminal alkynes are demonstrated.
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Affiliation(s)
- Kristina Streu
- Department of Chemistry, Haverford College, 370 Lancaster Ave., Haverford, Pennsylvania 19041, USA
| | - Sara Hunsberger
- Department of Chemistry, Haverford College, 370 Lancaster Ave., Haverford, Pennsylvania 19041, USA
| | - Jeanette Patel
- Department of Chemistry, Haverford College, 370 Lancaster Ave., Haverford, Pennsylvania 19041, USA
| | - Xiang Wan
- Department of Mathematics and Statistics, Loyola University Chicago, 1032 W. Sheridan Rd., Chicago, Illinois 60660, USA
| | - Clyde A Daly
- Department of Chemistry, Haverford College, 370 Lancaster Ave., Haverford, Pennsylvania 19041, USA
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7
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Yang EL, Talbot JJ, Spencer RJ, Steele RP. Pitfalls in the n-mode representation of vibrational potentials. J Chem Phys 2023; 159:204104. [PMID: 38010326 DOI: 10.1063/5.0176612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 10/19/2023] [Indexed: 11/29/2023] Open
Abstract
Simulations of anharmonic vibrational motion rely on computationally expedient representations of the governing potential energy surface. The n-mode representation (n-MR)-effectively a many-body expansion in the space of molecular vibrations-is a general and efficient approach that is often used for this purpose in vibrational self-consistent field (VSCF) calculations and correlated analogues thereof. In the present analysis, a lack of convergence in many VSCF calculations is shown to originate from negative and unbound potentials at truncated orders of the n-MR expansion. For cases of strong anharmonic coupling between modes, the n-MR can both dip below the true global minimum of the potential surface and lead to effective single-mode potentials in VSCF that do not correspond to bound vibrational problems, even for bound total potentials. The present analysis serves mainly as a pathology report of this issue. Furthermore, this insight into the origin of VSCF non-convergence provides a simple, albeit ad hoc, route to correct the problem by "painting in" the full representation of groups of modes that exhibit these negative potentials at little additional computational cost. Somewhat surprisingly, this approach also reasonably approximates the results of the next-higher n-MR order and identifies groups of modes with particularly strong coupling. The method is shown to identify and correct problematic triples of modes-and restore SCF convergence-in two-mode representations of challenging test systems, including the water dimer and trimer, as well as protonated tropine.
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Affiliation(s)
- Emily L Yang
- Department of Chemistry, The University of Utah, 315 S 1400 E, Salt Lake City, Utah 84112, USA
- Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, Utah 84112, USA
| | - Justin J Talbot
- Department of Chemistry, University of California-Berkeley, 420 Latimer Hall, Berkeley, California 94720, USA
| | - Ryan J Spencer
- Department of Chemistry, The University of Utah, 315 S 1400 E, Salt Lake City, Utah 84112, USA
- Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, Utah 84112, USA
| | - Ryan P Steele
- Department of Chemistry, The University of Utah, 315 S 1400 E, Salt Lake City, Utah 84112, USA
- Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, Utah 84112, USA
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8
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Erba A, Desmarais JK, Casassa S, Civalleri B, Donà L, Bush IJ, Searle B, Maschio L, Edith-Daga L, Cossard A, Ribaldone C, Ascrizzi E, Marana NL, Flament JP, Kirtman B. CRYSTAL23: A Program for Computational Solid State Physics and Chemistry. J Chem Theory Comput 2023; 19:6891-6932. [PMID: 36502394 PMCID: PMC10601489 DOI: 10.1021/acs.jctc.2c00958] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Indexed: 12/14/2022]
Abstract
The Crystal program for quantum-mechanical simulations of materials has been bridging the realm of molecular quantum chemistry to the realm of solid state physics for many years, since its first public version released back in 1988. This peculiarity stems from the use of atom-centered basis functions within a linear combination of atomic orbitals (LCAO) approach and from the corresponding efficiency in the evaluation of the exact Fock exchange series. In particular, this has led to the implementation of a rich variety of hybrid density functional approximations since 1998. Nowadays, it is acknowledged by a broad community of solid state chemists and physicists that the inclusion of a fraction of Fock exchange in the exchange-correlation potential of the density functional theory is key to a better description of many properties of materials (electronic, magnetic, mechanical, spintronic, lattice-dynamical, etc.). Here, the main developments made to the program in the last five years (i.e., since the previous release, Crystal17) are presented and some of their most noteworthy applications reviewed.
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Affiliation(s)
- Alessandro Erba
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Jacques K. Desmarais
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Silvia Casassa
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Bartolomeo Civalleri
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Lorenzo Donà
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Ian J. Bush
- STFC
Rutherford Appleton Laboratory, Chilton Didcot, Oxfordshire OX11 0QX, United Kingdom
| | - Barry Searle
- SFTC
Daresbury Laboratory, Daresbury, Cheshire WA4 4AD, United Kingdom
| | - Lorenzo Maschio
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Loredana Edith-Daga
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Alessandro Cossard
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Chiara Ribaldone
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Eleonora Ascrizzi
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Naiara L. Marana
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Jean-Pierre Flament
- Université
de Lille, CNRS, UMR 8523 — PhLAM — Physique des Lasers, Atomes et Molécules, 59000 Lille, France
| | - Bernard Kirtman
- Department
of Chemistry and Biochemistry, University
of California, Santa
Barbara, California 93106, United States
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9
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Zhanserkeev AA, Yang EL, Steele RP. Accelerating Anharmonic Spectroscopy Simulations via Local-Mode, Multilevel Methods. J Chem Theory Comput 2023; 19:5572-5585. [PMID: 37555634 DOI: 10.1021/acs.jctc.3c00589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Ab initio computer simulations of anharmonic vibrational spectra provide nuanced insight into the vibrational behavior of molecules and complexes. The computational bottleneck in such simulations, particularly for ab initio potentials, is often the generation of mode-coupling potentials. Focusing specifically on two-mode couplings in this analysis, the combination of a local-mode representation and multilevel methods is demonstrated to be particularly symbiotic. In this approach, a low-level quantum chemistry method is employed to predict the pairwise couplings that should be included at the target level of theory in vibrational self-consistent field (and similar) calculations. Pairs that are excluded by this approach are "recycled" at the low level of theory. Furthermore, because this low-level pre-screening will eventually become the computational bottleneck for sufficiently large chemical systems, distance-based truncation is applied to these low-level predictions without substantive loss of accuracy. This combination is demonstrated to yield sub-wavenumber fidelity with reference vibrational transitions when including only a small fraction of target-level couplings; the overhead of predicting these couplings, particularly when employing distance-based, local-mode cutoffs, is a trivial added cost. This combined approach is assessed on a series of test cases, including ethylene, hexatriene, and the alanine dipeptide. Vibrational self-consistent field (VSCF) spectra were obtained with an RI-MP2/cc-pVTZ potential for the dipeptide, at approximately a 5-fold reduction in computational cost. Considerable optimism for increased accelerations for larger systems and higher-order couplings is also justified, based on this investigation.
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Affiliation(s)
- Asylbek A Zhanserkeev
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Emily L Yang
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Ryan P Steele
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
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10
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Hanson-Heine MWD. Static Electron Correlation in Anharmonic Molecular Vibrations: A Hybrid TAO-DFT Study. J Phys Chem A 2022; 126:7273-7282. [PMID: 36164938 PMCID: PMC9574917 DOI: 10.1021/acs.jpca.2c05881] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Hybrid thermally-assisted-occupation density functional theory is used to examine the effects of static electron correlation on the prediction of a benchmark set of experimentally observed molecular vibrational frequencies. The B3LYP and B97-1 thermally-assisted-occupation measure of static electron correlation is important for describing the vibrations of many of the molecules that make up several popular test sets of experimental data. Shifts are seen for known multireference systems and for many molecules containing atoms from the second row of the periodic table of elements. Several molecules only show significant shifts in select vibrational modes, and significant improvements are seen for the prediction of hydrogen stretching frequencies throughout the test set.
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11
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Wu R, Matta M, Paulsen BD, Rivnay J. Operando Characterization of Organic Mixed Ionic/Electronic Conducting Materials. Chem Rev 2022; 122:4493-4551. [PMID: 35026108 DOI: 10.1021/acs.chemrev.1c00597] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Operando characterization plays an important role in revealing the structure-property relationships of organic mixed ionic/electronic conductors (OMIECs), enabling the direct observation of dynamic changes during device operation and thus guiding the development of new materials. This review focuses on the application of different operando characterization techniques in the study of OMIECs, highlighting the time-dependent and bias-dependent structure, composition, and morphology information extracted from these techniques. We first illustrate the needs, requirements, and challenges of operando characterization then provide an overview of relevant experimental techniques, including spectroscopy, scattering, microbalance, microprobe, and electron microscopy. We also compare different in silico methods and discuss the interplay of these computational methods with experimental techniques. Finally, we provide an outlook on the future development of operando for OMIEC-based devices and look toward multimodal operando techniques for more comprehensive and accurate description of OMIECs.
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Affiliation(s)
- Ruiheng Wu
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Micaela Matta
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, United Kingdom
| | - Bryan D Paulsen
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Jonathan Rivnay
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Simpson Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
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12
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Hanson-Heine MWD. Reduced Two-Electron Interactions in Anharmonic Molecular Vibrational Calculations Involving Localized Normal Coordinates. J Chem Theory Comput 2021; 17:4383-4391. [PMID: 34087068 DOI: 10.1021/acs.jctc.1c00314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Spatially localized vibrational normal mode coordinates are shown to reduce the importance of calculating the full set of two-electron terms in the molecular electronic Schrödinger equation. Electron correlation and dispersion interactions become less significant in (E,E)-1,3,5,7-octatetraene vibrational self-consistent field calculations when displacing remote atoms along multiple coordinates. Electron correlation interactions between spatially remote modes are also found to be less important compared to their corresponding uncorrelated interaction terms. Attenuation of the Coulomb operator indicates that the two-electron terms between remote electrons become less important for accurately describing the strongly contributing mode-coupling terms between sets of localized vibrational modes.
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13
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Fan J, Su Y, Zheng Z, Zhao J. Thermal properties of energetic materials from quasi-harmonic first-principles calculations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 33:275702. [PMID: 33906164 DOI: 10.1088/1361-648x/abfc11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/27/2021] [Indexed: 06/12/2023]
Abstract
The structure and properties at a finite temperature are critical to understand the temperature effects on energetic materials (EMs). Combining dispersion-corrected density functional theory with quasi-harmonic approximation, the thermodynamic properties for several representative EMs, including nitromethane, PETN, HMX, and TATB, are calculated. The inclusion of zero-point energy and temperature effect could significantly improve the accuracy of lattice parameters at ambient condition; the deviations of calculated cell volumes and experimental values at room temperature are within 0.62%. The calculated lattice parameters and thermal expansion coefficients with increasing temperature show strong anisotropy. In particular, the expansion rate (2.61%) of inter-layer direction of TATB is higher than intra-layer direction and other EMs. Furthermore, the calculated heat capacities could reproduce the experimental trends and enrich the thermodynamic data set at finite temperatures. The predicted isothermal and adiabatic bulk moduli could reflect the softening behavior of EMs. These results would fundamentally provide a deep understanding and serve as a reference for the experimental measurement of the thermodynamic parameters of EMs.
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Affiliation(s)
- Junyu Fan
- Key Laboratory of Materials Modification by Laser, Ion and Electron Beams (Dalian University of Technology), Ministry of Education, Dalian 116024, People's Republic of China
- Department of Physics, Taiyuan Normal University, Jinzhong 030619, People's Republic of China
- Institute of Computational and Applied Physics, Taiyuan Normal University, Jinzhong 030619, People's Republic of China
| | - Yan Su
- Key Laboratory of Materials Modification by Laser, Ion and Electron Beams (Dalian University of Technology), Ministry of Education, Dalian 116024, People's Republic of China
| | - Zhaoyang Zheng
- National Key Laboratory of Shock Wave and Detonation Physics, Institute of Fluid Physics, China Academy of Engineering Physics, Mianyang 621900, People's Republic of China
| | - Jijun Zhao
- Key Laboratory of Materials Modification by Laser, Ion and Electron Beams (Dalian University of Technology), Ministry of Education, Dalian 116024, People's Republic of China
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14
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Ermiş B, Ünal A, Soydaş E, Bozkaya U. Anharmonic force field from coupled-cluster methods and accurate computation of infrared spectra. ADVANCES IN QUANTUM CHEMISTRY 2021. [DOI: 10.1016/bs.aiq.2021.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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15
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Hanson-Heine MW. Static correlation in vibrational frequencies studied using thermally-assisted-occupation density functional theory. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2019.137012] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Hanson-Heine MWD. Benchmarking DFT-D Dispersion Corrections for Anharmonic Vibrational Frequencies and Harmonic Scaling Factors. J Phys Chem A 2019; 123:9800-9808. [PMID: 31633366 DOI: 10.1021/acs.jpca.9b07886] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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17
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Harabuchi Y, Tani R, De Silva N, Njegic B, Gordon MS, Taketsugu T. Anharmonic vibrational computations with a quartic force field for curvilinear coordinates. J Chem Phys 2019. [DOI: 10.1063/1.5096167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yu Harabuchi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Ryosuke Tani
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Nuwan De Silva
- Department of Physical and Biological Sciences, Western New England University, Springfield, Massachusetts 01119, USA
| | - Bosiljka Njegic
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
| | - Mark S. Gordon
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
| | - Tetsuya Taketsugu
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan
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18
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Erba A, Maul J, Ferrabone M, Carbonnière P, Rérat M, Dovesi R. Anharmonic Vibrational States of Solids from DFT Calculations. Part I: Description of the Potential Energy Surface. J Chem Theory Comput 2019; 15:3755-3765. [DOI: 10.1021/acs.jctc.9b00293] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alessandro Erba
- Dipartimento di Chimica, Universitá di Torino, via Giuria 5, 10125 Torino, Italy
| | - Jefferson Maul
- Dipartimento di Chimica, Universitá di Torino, via Giuria 5, 10125 Torino, Italy
| | - Matteo Ferrabone
- Dipartimento di Chimica, Universitá di Torino, via Giuria 5, 10125 Torino, Italy
| | - Philippe Carbonnière
- IPREM, Université de Pau et des Pays de l’Adour, IPREM-CAPT UMR CNRS 5254, Hélioparc Pau Pyrénées, 2 avenue du Président Angot, 64053 PAU CEDEX 9, Pau, France
| | - Michel Rérat
- IPREM, Université de Pau et des Pays de l’Adour, IPREM-CAPT UMR CNRS 5254, Hélioparc Pau Pyrénées, 2 avenue du Président Angot, 64053 PAU CEDEX 9, Pau, France
| | - Roberto Dovesi
- Dipartimento di Chimica, Universitá di Torino, via Giuria 5, 10125 Torino, Italy
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19
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Sethio D, Oliveira V, Kraka E. Quantitative Assessment of Tetrel Bonding Utilizing Vibrational Spectroscopy. Molecules 2018; 23:E2763. [PMID: 30366391 PMCID: PMC6278569 DOI: 10.3390/molecules23112763] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 10/19/2018] [Accepted: 10/20/2018] [Indexed: 01/15/2023] Open
Abstract
A set of 35 representative neutral and charged tetrel complexes was investigated with the objective of finding the factors that influence the strength of tetrel bonding involving single bonded C, Si, and Ge donors and double bonded C or Si donors. For the first time, we introduced an intrinsic bond strength measure for tetrel bonding, derived from calculated vibrational spectroscopy data obtained at the CCSD(T)/aug-cc-pVTZ level of theory and used this measure to rationalize and order the tetrel bonds. Our study revealed that the strength of tetrel bonds is affected by several factors, such as the magnitude of the σ-hole in the tetrel atom, the negative electrostatic potential at the lone pair of the tetrel-acceptor, the positive charge at the peripheral hydrogen of the tetrel-donor, the exchange-repulsion between the lone pair orbitals of the peripheral atoms of the tetrel-donor and the heteroatom of the tetrel-acceptor, and the stabilization brought about by electron delocalization. Thus, focusing on just one or two of these factors, in particular, the σ-hole description can only lead to an incomplete picture. Tetrel bonding covers a range of -1.4 to -26 kcal/mol, which can be strengthened by substituting the peripheral ligands with electron-withdrawing substituents and by positively charged tetrel-donors or negatively charged tetrel-acceptors.
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Affiliation(s)
- Daniel Sethio
- Computational and Theoretical Chemistry Group, Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, TX 75275-0314, USA.
| | - Vytor Oliveira
- Computational and Theoretical Chemistry Group, Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, TX 75275-0314, USA.
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group, Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, TX 75275-0314, USA.
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20
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Hanson-Heine MW, Calladine JA, Yang J, Towrie M, Horvath R, Besley NA, George MW. A combined time-resolved infrared and density functional theory study of the lowest excited states of 9-fluorenone and 2-naphthaldehyde. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.04.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Hanson-Heine MWD. Reduced Basis Set Dependence in Anharmonic Frequency Calculations Involving Localized Coordinates. J Chem Theory Comput 2018; 14:1277-1285. [PMID: 29385338 DOI: 10.1021/acs.jctc.7b01075] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Localized normal coordinates are known to be effective in speeding up anharmonic frequency calculations by reducing the complexity of the nuclear Hamiltonian and wave function. Displacing atoms in localized coordinates can also cause relatively small changes in the electronic structure, which can be exploited for further computational efficiency improvements during ab initio electronic structure calculations of the potential energy surface by reducing the electronic basis set dependence. Three different schemes for reducing the basis set dependence have been investigated in this work. These include combining localized coordinate schemes with general mixed basis sets, distance based force-field reductions, and using coordinate specific basis sets. The importance of accurately describing electronic interactions is found to diminish both for multicoordinate terms involving the displacement of remote atoms and when describing the interactions between more remote atoms within specific coordinates.
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22
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Sharma S, Wright TG, Besley NA. Reactivity of the O2+·(H2O)n and NO+·(H2O)n cluster ions in the D-region of the ionosphere. Phys Chem Chem Phys 2018; 20:25931-25938. [DOI: 10.1039/c8cp05681a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ab initio molecular dynamics simulations reveal different reactivities of NO+·(H2O)n and O2+·(H2O)n cluster ions in the D-region of the ionosphere.
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23
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Chien AD, Zimmerman PM. Iterative submatrix diagonalisation for large configuration interaction problems. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1368727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Alan D. Chien
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
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24
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Hanson-Heine MWD. Intermediate vibrational coordinate localization with harmonic coupling constraints. J Chem Phys 2017; 144:204116. [PMID: 27250288 DOI: 10.1063/1.4951011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Optimized normal coordinates can significantly improve the speed and accuracy of vibrational frequency calculations. However, over-localization can occur when using unconstrained spatial localization techniques. The unintuitive mixtures of stretching and bending coordinates that result can make interpreting spectra more difficult and also cause artificial increases in mode-coupling during anharmonic calculations. Combining spatial localization with a constraint on the coupling between modes can be used to generate coordinates with properties in-between the normal and fully localized schemes. These modes preserve the diagonal nature of the mass-weighted Hessian matrix to within a specified tolerance and are found to prevent contamination between the stretching and bending vibrations of the molecules studied without a priori classification of the different types of vibration present. Relaxing the constraint can also be used to identify which normal modes form specific groups of localized modes. The new coordinates are found to center on more spatially delocalized functional groups than their fully localized counterparts and can be used to tune the degree of vibrational correlation energy during anharmonic calculations.
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Affiliation(s)
- Magnus W D Hanson-Heine
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
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25
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Gentile FS, Salustro S, Causà M, Erba A, Carbonniére P, Dovesi R. The VN3H defect in diamond: a quantum-mechanical characterization. Phys Chem Chem Phys 2017; 19:22221-22229. [DOI: 10.1039/c7cp03957c] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structural, electronic, energetic and vibrational spectroscopic (IR and Raman) properties of the VN3H defect in diamond are investigated with quantum mechanical simulations.
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Affiliation(s)
| | - Simone Salustro
- Dipartimento di Chimica
- Università di Torino
- IT-10125 Torino
- Italy
| | - Mauro Causà
- Dipartimento di Ingengeria Chimica
- dei Materiali e delle Produzioni Industriali DICMAPI
- Università degli Studi di Napoli Federico II
- Napoli
- Italy
| | - Alessandro Erba
- Dipartimento di Chimica
- Università di Torino
- IT-10125 Torino
- Italy
| | - Philippe Carbonniére
- Equipe de Chimie Physique
- IPREM UMR5254
- Université de Pau et des Pays de l'Adour
- 64000 Pau
- France
| | - Roberto Dovesi
- Dipartimento di Chimica
- Università di Torino
- IT-10125 Torino
- Italy
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26
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Delgado-Venegas RI, Mejía-Rodríguez D, Flores-Moreno R, Calaminici P, Köster AM. Analytic second derivatives from auxiliary density perturbation theory. J Chem Phys 2016; 145:224103. [PMID: 27984884 DOI: 10.1063/1.4971292] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Rogelio Isaac Delgado-Venegas
- Departamento de Química, CINVESTAV, Avenida Instituto Politécnico Nacional 2508, A.P. 14-740, México D.F. 07000, Mexico
| | - Daniel Mejía-Rodríguez
- Departamento de Química, CINVESTAV, Avenida Instituto Politécnico Nacional 2508, A.P. 14-740, México D.F. 07000, Mexico
| | - Roberto Flores-Moreno
- Departamento de Química, Universidad de Guadalajara, Boulevard Marcelino García Barragán 1421, Guadalajara, Jalisco 44430, Mexico
| | - Patrizia Calaminici
- Departamento de Química, CINVESTAV, Avenida Instituto Politécnico Nacional 2508, A.P. 14-740, México D.F. 07000, Mexico
| | - Andreas M. Köster
- Departamento de Química, CINVESTAV, Avenida Instituto Politécnico Nacional 2508, A.P. 14-740, México D.F. 07000, Mexico
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27
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Erba A, Maul J, Civalleri B. Thermal properties of molecular crystals through dispersion-corrected quasi-harmonic ab initio calculations: the case of urea. Chem Commun (Camb) 2016; 52:1820-3. [PMID: 26670006 DOI: 10.1039/c5cc08982d] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An ab initio quantum-mechanical theoretical framework is presented to compute the thermal properties of molecular crystals. The present strategy combines dispersion-corrected density-functional-theory (DFT-D), harmonic phonon dispersion, quasi-harmonic approximation to the lattice dynamics for thermal expansion and thermodynamic functions, and quasi-static approximation for anisotropic thermo-elasticity. The proposed scheme is shown to reliably describe thermal properties of the urea molecular crystal by a thorough comparison with experimental data.
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Affiliation(s)
- Alessandro Erba
- Dipartimento di Chimica, Università di Torino and Interdepartmental Centre NIS, Nanostructured Interfaces and Surfaces, Via Giuria 5, 10125 Torino, Italy.
| | - Jefferson Maul
- Dipartimento di Chimica, Università di Torino and Interdepartmental Centre NIS, Nanostructured Interfaces and Surfaces, Via Giuria 5, 10125 Torino, Italy. and Laboratório de Combustíveis e Materiais, INCTMN-UFPB, Universidade Federal da Paraíba, CEP 58051-900, João Pessoa, PB, Brazil
| | - Bartolomeo Civalleri
- Dipartimento di Chimica, Università di Torino and Interdepartmental Centre NIS, Nanostructured Interfaces and Surfaces, Via Giuria 5, 10125 Torino, Italy.
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28
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Sadoon AM, Sarma G, Cunningham EM, Tandy J, Hanson-Heine MWD, Besley NA, Yang S, Ellis AM. Infrared Spectroscopy of NaCl(CH3OH)n Complexes in Helium Nanodroplets. J Phys Chem A 2016; 120:8085-8092. [DOI: 10.1021/acs.jpca.6b06227] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ahmed M. Sadoon
- Department
of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
- Department
of Chemistry, College for Pure Sciences, University of Mosul, Mosul, Iraq
| | - Gautam Sarma
- Department
of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | - Ethan M. Cunningham
- Department
of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | - Jon Tandy
- Department
of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | | | - Nicholas A. Besley
- School
of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Shengfu Yang
- Department
of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | - Andrew M. Ellis
- Department
of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
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29
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Hanson-Heine MWD. Examining the impact of harmonic correlation on vibrational frequencies calculated in localized coordinates. J Chem Phys 2016; 143:164104. [PMID: 26520495 DOI: 10.1063/1.4934234] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Carefully choosing a set of optimized coordinates for performing vibrational frequency calculations can significantly reduce the anharmonic correlation energy from the self-consistent field treatment of molecular vibrations. However, moving away from normal coordinates also introduces an additional source of correlation energy arising from mode-coupling at the harmonic level. The impact of this new component of the vibrational energy is examined for a range of molecules, and a method is proposed for correcting the resulting self-consistent field frequencies by adding the full coupling energy from connected pairs of harmonic and pseudoharmonic modes, termed vibrational self-consistent field (harmonic correlation). This approach is found to lift the vibrational degeneracies arising from coordinate optimization and provides better agreement with experimental and benchmark frequencies than uncorrected vibrational self-consistent field theory without relying on traditional correlated methods.
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Affiliation(s)
- Magnus W D Hanson-Heine
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
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30
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Zimmerman PM, Smereka P. Optimizing Vibrational Coordinates To Modulate Intermode Coupling. J Chem Theory Comput 2016; 12:1883-91. [PMID: 26914536 DOI: 10.1021/acs.jctc.5b01168] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The choice of coordinate system strongly affects the convergence properties of vibrational structure computations. Two methods for efficient generation of improved vibrational coordinates are presented and justified by analysis of a model anharmonic two-mode Hessian and numerical computations on polyatomic molecules. To produce optimal coordinates, metrics which quantify off-diagonal couplings over a grid of Hessian matrices are minimized through unitary rotations of the vibrational basis. The first proposed metric minimizes the total squared off-diagonal coupling, and the second minimizes the total squared change in off-diagonal coupling. In this procedure certain anharmonic modes tend to localize, for example X-H stretches. The proposed methods do not rely on prior fitting of the potential energy, vibrational structure computations, or localization metrics, so they are unique from previous vibrational coordinate generation algorithms and are generally applicable to polyatomic molecules. Fitting the potential to the approximate n-mode representation in the optimized bases for all-trans polyenes shows that off-diagonal anharmonic couplings are substantially reduced by the new choices of coordinate system. Convergence of vibrational energies is examined in detail for ethylene, and it is shown that coupling-optimized modes converge in vibrational configuration interaction computations to within 1 cm(-1) using only 3-mode couplings, where normal modes require 4-mode couplings for convergence. Comparison of the vibrational configuration interaction convergence with respect to excitation level for the two proposed metrics shows that minimization of the total off-diagonal coupling is most effective for low-cost vibrational structure computations.
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Affiliation(s)
- Paul M Zimmerman
- Department of Chemistry and ‡Department of Mathematics, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Peter Smereka
- Department of Chemistry and ‡Department of Mathematics, University of Michigan , Ann Arbor, Michigan 48109, United States
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31
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Yagi K. Development of Molecular Vibrational Structure Theory with an Explicit Account of Anharmonicity. ACTA ACUST UNITED AC 2016. [DOI: 10.3175/molsci.10.a0085] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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32
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Quantum chemical calculations and analysis of FTIR, FT–Raman and UV–Vis spectra of temozolomide molecule. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.07.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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33
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Sibaev M, Crittenden DL. The PyPES library of high quality semi-global potential energy surfaces. J Comput Chem 2015; 36:2200-7. [DOI: 10.1002/jcc.24192] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 07/19/2015] [Accepted: 08/10/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Marat Sibaev
- Department of Chemistry; University of Canterbury; Christchurch New Zealand
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34
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Erba A. On combining temperature and pressure effects on structural properties of crystals with standard ab initio techniques. J Chem Phys 2015; 141:124115. [PMID: 25273420 DOI: 10.1063/1.4896228] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A general-purpose, fully automated, computationally efficient implementation is presented of a series of techniques for the simultaneous description of pressure and temperature effects on structural properties of materials, by means of standard ab initio simulations. Equilibrium volume, bulk modulus, thermal expansion coefficient, equation-of-state, Grüneisen parameter, constant-pressure and constant-volume specific heats are computed as a function of temperature and pressure for the simple crystal of diamond and compared with accurate experimental data. Convergence of computed properties with respect to super-cell size is critically discussed. The effect on such properties of the adopted exchange-correlation functional of the density-functional-theory is discussed by considering three different levels of approximation (including hybrids): it is found to be rather small for the temperature dependence of equilibrium volume and bulk modulus, whereas it is quite large as regards their absolute values.
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Affiliation(s)
- A Erba
- Dipartimento di Chimica and Centre of Excellence NIS (Nanostructured Interfaces and Surfaces), Università di Torino, via Giuria 5, IT-10125 Torino, Italy
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35
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Do H, Besley NA. Calculation of the vibrational frequencies of carbon clusters and fullerenes with empirical potentials. Phys Chem Chem Phys 2015; 17:3898-908. [DOI: 10.1039/c4cp05424e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Empirical potentials are assessed and optimized for the calculation of the vibrational frequencies of fullerenes and nanotubes.
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Affiliation(s)
- Hainam Do
- School of Chemistry
- University of Nottingham
- University Park
- Nottingham
- UK
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36
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König G, Hudson PS, Boresch S, Woodcock HL. Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes. J Chem Theory Comput 2014; 10:1406-1419. [PMID: 24803863 PMCID: PMC3985817 DOI: 10.1021/ct401118k] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Indexed: 11/28/2022]
Abstract
![]()
The reliability of free energy simulations
(FES) is limited by
two factors: (a) the need for correct sampling and (b) the accuracy
of the computational method employed. Classical methods (e.g., force
fields) are typically used for FES and present a myriad of challenges,
with parametrization being a principle one. On the other hand, parameter-free
quantum mechanical (QM) methods tend to be too computationally expensive
for adequate sampling. One widely used approach is a combination of
methods, where the free energy difference between the two end states
is computed by, e.g., molecular mechanics (MM), and the end states
are corrected by more accurate methods, such as QM or hybrid QM/MM
techniques. Here we report two new approaches that significantly improve
the aforementioned scheme; with a focus on how to compute corrections
between, e.g., the MM and the more accurate QM calculations. First,
a molecular dynamics trajectory that properly samples relevant conformational
degrees of freedom is generated. Next, potential energies of each
trajectory frame are generated with a QM or QM/MM Hamiltonian. Free
energy differences are then calculated based on the QM or QM/MM energies
using either a non-Boltzmann Bennett approach (QM-NBB) or non-Boltzmann
free energy perturbation (NB-FEP). Both approaches are applied to
calculate relative and absolute solvation free energies in explicit
and implicit solvent environments. Solvation free energy differences
(relative and absolute) between ethane and methanol in explicit solvent
are used as the initial test case for QM-NBB. Next, implicit solvent
methods are employed in conjunction with both QM-NBB and NB-FEP to
compute absolute solvation free energies for 21 compounds. These compounds
range from small molecules such as ethane and methanol to fairly large,
flexible solutes, such as triacetyl glycerol. Several technical aspects
were investigated. Ultimately some best practices are suggested for
improving methods that seek to connect MM to QM (or QM/MM) levels
of theory in FES.
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Affiliation(s)
- Gerhard König
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Phillip S Hudson
- Department of Chemistry, University of South Florida , 4202 E. Fowler Avenue, CHE205, Tampa, Florida 33620-5250, United States
| | - Stefan Boresch
- Department of Computational Biological Chemistry, Faculty of Chemistry, University of Vienna , Währingerstraße 17, A-1090 Vienna, Austria
| | - H Lee Woodcock
- Department of Chemistry, University of South Florida , 4202 E. Fowler Avenue, CHE205, Tampa, Florida 33620-5250, United States
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37
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Hanson-Heine MWD, George MW, Besley NA. Calculating excited state properties using Kohn-Sham density functional theory. J Chem Phys 2013; 138:064101. [PMID: 23425455 DOI: 10.1063/1.4789813] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The accuracy of excited states calculated with Kohn-Sham density functional theory using the maximum overlap method has been assessed for the calculation of adiabatic excitation energies, excited state structures, and excited state harmonic and anharmonic vibrational frequencies for open-shell singlet excited states. The computed Kohn-Sham adiabatic excitation energies are improved significantly by post self-consistent field spin-purification, but remain too low compared with experiment with a larger error than time-dependent density functional theory. Excited state structures and vibrational frequencies are also improved by spin-purification. The structures show a comparable accuracy to time-dependent density functional theory, while the harmonic vibrational frequencies are found to be more accurate for the majority of vibrational modes. The computed harmonic vibrational frequencies are also further improved by perturbative anharmonic corrections, suggesting a good description of the potential energy surface. Overall, excited state Kohn-Sham density functional theory is shown to provide an efficient method for the calculation of excited state structures and vibrational frequencies in open-shell singlet systems and provides a promising technique that can be applied to study large systems.
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Affiliation(s)
- Magnus W D Hanson-Heine
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
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38
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Rosnik AM, Polik WF. VPT2+K spectroscopic constants and matrix elements of the transformed vibrational Hamiltonian of a polyatomic molecule with resonances using Van Vleck perturbation theory. Mol Phys 2013. [DOI: 10.1080/00268976.2013.808386] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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39
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Arruda MS, Marinho RRT, Maniero AM, Mundin MSP, Mocellin A, Pilling S, de Brito AN, Prudente FV. Theoretical-experimental study of formic acid photofragmentation in the valence region. J Phys Chem A 2012; 116:6693-701. [PMID: 22606986 DOI: 10.1021/jp209259j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photoionization and photofragmentation studies of formic acid (HCOOH) are performed for the valence shell electron ionization process. The total and partial ion yield of gaseous HCOOH were collected as a function of photon energy in the ultraviolet region, between 11.12 and 19.57 eV. Measurements of the total and partial ion yield of gaseous formic acid molecule are performed with a time-of-flight mass spectrometer at the Synchrotron Light Brazilian Laboratory. Density functional theory and time dependent density functional theory are employed to calculate the ground and excited electronic state energies of neutral and ionic formic acid as well as their fragments and normal vibration modes. The ionization potential energies, the stability of electronic excited states of HCOOH(+), and the energies of opening fragmentation channels are estimated from theoretical-experimental analysis. Additionally, the main formic acid photofragmentation pathways by exposition of photons within that energy range are determined experimentally. These produced ions primarily have the following mass/charge ratios: 46 (HCOOH(+)), 45 (COOH(+)), 29 (HCO(+)), and 18 (H(2)O(+)).
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Affiliation(s)
- Manuela S Arruda
- Instituto de Física, Universidade Federal da Bahia, 40210-340 Salvador, BA, Brazil
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40
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Hanson-Heine MWD, George MW, Besley NA. Rapid anharmonic vibrational corrections derived from partial Hessian analysis. J Chem Phys 2012; 136:224102. [DOI: 10.1063/1.4727853] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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41
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Hanson-Heine MWD, George MW, Besley NA. Investigating the Calculation of Anharmonic Vibrational Frequencies Using Force Fields Derived from Density Functional Theory. J Phys Chem A 2012; 116:4417-25. [DOI: 10.1021/jp301670f] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
| | - Michael W. George
- School of Chemistry, University of Nottingham, University Park, Nottingham
NG7 2RD, U.K
| | - Nicholas A. Besley
- School of Chemistry, University of Nottingham, University Park, Nottingham
NG7 2RD, U.K
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42
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Van-Oanh NT, Falvo C, Calvo F, Lauvergnat D, Basire M, Gaigeot MP, Parneix P. Improving anharmonic infrared spectra using semiclassically prepared molecular dynamics simulations. Phys Chem Chem Phys 2012; 14:2381-90. [DOI: 10.1039/c2cp23101h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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43
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Lambrecht DS, Clark GNI, Head-Gordon T, Head-Gordon M. Exploring the Rich Energy Landscape of Sulfate–Water Clusters SO42– (H2O)n=3–7: An Electronic Structure Approach. J Phys Chem A 2011; 115:11438-54. [DOI: 10.1021/jp206064n] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Daniel S. Lambrecht
- Department of Chemistry and ‡Department of Bioengineering, University of California, Berkeley, California
- Physical Biosciences Division and ∥Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Gary N. I. Clark
- Department of Chemistry and ‡Department of Bioengineering, University of California, Berkeley, California
- Physical Biosciences Division and ∥Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Teresa Head-Gordon
- Department of Chemistry and ‡Department of Bioengineering, University of California, Berkeley, California
- Physical Biosciences Division and ∥Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Martin Head-Gordon
- Department of Chemistry and ‡Department of Bioengineering, University of California, Berkeley, California
- Physical Biosciences Division and ∥Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California
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Ringer AL, MacKerell AD. Calculation of the Vibrational Stark Effect Using a First-Principles QM/MM Approach. J Phys Chem Lett 2011; 2011:553-556. [PMID: 21423871 PMCID: PMC3058488 DOI: 10.1021/jz101657s] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The proper description of the electric environment of condensed phases is a critical challenge for force field methods. To test and validate the ability of the CHARMM additive force field to describe the electric environment in aqueous solution combined QM/MM calculations have been used to calculate the vibrational Stark effect (VSE). We utilized a first principles methodology using correlated electronic structure techniques to compute the Stark shift between the gas phase and solvent environments and between two different solvent environments of three VSE probes containing acetonitrile or fluorine functionalities which have been well-characterized experimentally. Reasonable agreement with the experimentally determined Stark shifts is obtained when the MM atoms are described by the CHARMM additive force field, though it is essential to employ an anharmonic correction in the frequency calculation. In addition, the electric field created by the solvent is computed along the CN bond and a theoretical Stark tuning rate is determined for acetonitrile and shown to be in satisfactory agreement with experiment.
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Rasheed T, Ahmad S. Approximate solution of the mode-mode coupling integral: Application to cytosine and its deuterated derivative. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2010; 77:446-456. [PMID: 20638327 DOI: 10.1016/j.saa.2010.06.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Revised: 05/30/2010] [Accepted: 06/11/2010] [Indexed: 05/29/2023]
Abstract
Ab initio Hartree-Fock (HF), density functional theory (DFT) and second-order Møller-Plesset (MP2) methods were used to perform harmonic and anharmonic calculations for the biomolecule cytosine and its deuterated derivative. The anharmonic vibrational spectra were computed using the vibrational self-consistent field (VSCF) and correlation-corrected vibrational self-consistent field (CC-VSCF) methods. Calculated anharmonic frequencies have been compared with the argon matrix spectra reported in literature. The results were analyzed with focus on the properties of anharmonic couplings between pair of modes. A simple and easy to use formula for calculation of mode-mode coupling magnitudes has been derived. The key element in present approach is the approximation that only interactions between pairs of normal modes have been taken into account, while interactions of triples or more are neglected. FTIR and Raman spectra of solid state cytosine have been recorded in the regions 400-4000 cm(-1) and 60-4000 cm(-1), respectively. Vibrational analysis and assignments are based on calculated potential energy distribution (PED) values.
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Affiliation(s)
- Tabish Rasheed
- Department of Physics, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India
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Bégué D, Baraille I, Garrain PA, Dargelos A, Tassaing T. Calculation of IR frequencies and intensities in electrical and mechanical anharmonicity approximations: Application to small water clusters. J Chem Phys 2010; 133:034102. [DOI: 10.1063/1.3457482] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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48
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Baiz CR, McRobbie PL, Preketes NK, Kubarych KJ, Geva E. Two-Dimensional Infrared Spectroscopy of Dimanganese Decacarbonyl and Its Photoproducts: An Ab Initio Study. J Phys Chem A 2009; 113:9617-23. [DOI: 10.1021/jp9054654] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Carlos R. Baiz
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | | | | | - Kevin J. Kubarych
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Eitan Geva
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
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Erba A, Casassa S, Dovesi R, Maschio L, Pisani C. Periodic density functional theory and local-MP2 study of the librational modes of Ice XI. J Chem Phys 2009; 130:074505. [DOI: 10.1063/1.3076921] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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50
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A local-MP2 approach to the ab initio study of electron correlation in crystals and to the simulation of vibrational spectra: the case of Ice XI. Theor Chem Acc 2009. [DOI: 10.1007/s00214-009-0512-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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