1
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Bautista-Renedo J, Ireta J. Spurious proton transfer in hydrogen bonded dimers. Phys Chem Chem Phys 2024; 26:21468-21475. [PMID: 39081021 DOI: 10.1039/d4cp00907j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
In some hydrogen bonded systems, the proton may translocate along the hydrogen bond (hb) upon geometry optimization with electronic structure methods like density functional theory (DFT). Such proton transfer (pt) events, however, may be spurious. In this work, spurious pt events are investigated in a set of hydrogen bonded dimers formed with molecules HXN, where X stands for C, Si, Ge and Sn. It is found that standard approximations to the electronic exchange and correlation (xc) functional either predict spurious pt events or too strong hbs in all the (HXN)2 dimers except the (HCN)2 one. The latter result is revealed by comparing DFT calculations against wave function methods. Such spurious pt events may be avoided by fine-tuning the percentage of exact exchange (ex) in hybrid xc-functionals. It is shown that the minimum amount of ex to avoid a spurious pt event ranged from 8% to 90%, depending on the system, basis set and xc-functional approximation used. However, these fine-tuned xc-functionals inadequately describe the hb in the (HXN)2 dimers. Moreover, it is determined that the spurious pt event originates from a wrong description of the isolated HXN molecules by xc-functionals that do not include ex or a small amount of it. Therefore, it is argued that one can determine if a pt event is spurious by analyzing the geometry and electronic structure of the isolated molecule.
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Affiliation(s)
- Joanatan Bautista-Renedo
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, Ciudad de México 09340, Mexico.
| | - Joel Ireta
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, Ciudad de México 09340, Mexico.
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2
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Troß J, Arias-Martinez JE, Carter-Fenk K, Cole-Filipiak NC, Schrader P, McCaslin LM, Head-Gordon M, Ramasesha K. Femtosecond Core-Level Spectroscopy Reveals Involvement of Triplet States in the Gas-Phase Photodissociation of Fe(CO) 5. J Am Chem Soc 2024; 146:22711-22723. [PMID: 39092878 DOI: 10.1021/jacs.4c07523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Excitation of iron pentacarbonyl [Fe(CO)5], a prototypical photocatalyst, at 266 nm causes the sequential loss of two CO ligands in the gas phase, creating catalytically active, unsaturated iron carbonyls. Despite numerous studies, major aspects of its ultrafast photochemistry remain unresolved because the early excited-state dynamics have so far eluded spectroscopic observation. This has led to the long-held assumption that ultrafast dissociation of gas-phase Fe(CO)5 proceeds exclusively on the singlet manifold. Herein, we present a combined experimental-theoretical study employing ultrafast extreme ultraviolet transient absorption spectroscopy near the Fe M2,3-edge, which features spectral evolution on 100 fs and 3 ps time scales, alongside high-level electronic structure theory, which enables characterization of the molecular geometries and electronic states involved in the ultrafast photodissociation of Fe(CO)5. We assign the 100 fs evolution to spectroscopic signatures associated with intertwined structural and electronic dynamics on the singlet metal-centered states during the first CO loss and the 3 ps evolution to the competing dissociation of Fe(CO)4 along the lowest singlet and triplet surfaces to form Fe(CO)3. Calculations of transient spectra in both singlet and triplet states as well as spin-orbit coupling constants along key structural pathways provide evidence for intersystem crossing to the triplet ground state of Fe(CO)4. Thus, our work presents the first spectroscopic detection of transient excited states during ultrafast photodissociation of gas-phase Fe(CO)5 and challenges the long-standing assumption that triplet states do not play a role in the ultrafast dynamics.
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Affiliation(s)
- Jan Troß
- Combustion Research Facility, Sandia National Laboratories, Livermore, California 94550, United States
| | - Juan E Arias-Martinez
- Kenneth S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Kevin Carter-Fenk
- Kenneth S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Neil C Cole-Filipiak
- Combustion Research Facility, Sandia National Laboratories, Livermore, California 94550, United States
| | - Paul Schrader
- Combustion Research Facility, Sandia National Laboratories, Livermore, California 94550, United States
| | - Laura M McCaslin
- Combustion Research Facility, Sandia National Laboratories, Livermore, California 94550, United States
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Krupa Ramasesha
- Combustion Research Facility, Sandia National Laboratories, Livermore, California 94550, United States
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3
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Cao Y, Balduf T, Beachy MD, Bennett MC, Bochevarov AD, Chien A, Dub PA, Dyall KG, Furness JW, Halls MD, Hughes TF, Jacobson LD, Kwak HS, Levine DS, Mainz DT, Moore KB, Svensson M, Videla PE, Watson MA, Friesner RA. Quantum chemical package Jaguar: A survey of recent developments and unique features. J Chem Phys 2024; 161:052502. [PMID: 39092934 DOI: 10.1063/5.0213317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 07/12/2024] [Indexed: 08/04/2024] Open
Abstract
This paper is dedicated to the quantum chemical package Jaguar, which is commercial software developed and distributed by Schrödinger, Inc. We discuss Jaguar's scientific features that are relevant to chemical research as well as describe those aspects of the program that are pertinent to the user interface, the organization of the computer code, and its maintenance and testing. Among the scientific topics that feature prominently in this paper are the quantum chemical methods grounded in the pseudospectral approach. A number of multistep workflows dependent on Jaguar are covered: prediction of protonation equilibria in aqueous solutions (particularly calculations of tautomeric stability and pKa), reactivity predictions based on automated transition state search, assembly of Boltzmann-averaged spectra such as vibrational and electronic circular dichroism, as well as nuclear magnetic resonance. Discussed also are quantum chemical calculations that are oriented toward materials science applications, in particular, prediction of properties of optoelectronic materials and organic semiconductors, and molecular catalyst design. The topic of treatment of conformations inevitably comes up in real world research projects and is considered as part of all the workflows mentioned above. In addition, we examine the role of machine learning methods in quantum chemical calculations performed by Jaguar, from auxiliary functions that return the approximate calculation runtime in a user interface, to prediction of actual molecular properties. The current work is second in a series of reviews of Jaguar, the first having been published more than ten years ago. Thus, this paper serves as a rare milestone on the path that is being traversed by Jaguar's development in more than thirty years of its existence.
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Affiliation(s)
- Yixiang Cao
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Ty Balduf
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Michael D Beachy
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - M Chandler Bennett
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Art D Bochevarov
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Alan Chien
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Pavel A Dub
- Schrödinger, Inc., 9868 Scranton Road, Suite 3200, San Diego, California 92121, USA
| | - Kenneth G Dyall
- Schrödinger, Inc., 101 SW Main St., Suite 1300, Portland, Oregon 97204, USA
| | - James W Furness
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Mathew D Halls
- Schrödinger, Inc., 9868 Scranton Road, Suite 3200, San Diego, California 92121, USA
| | - Thomas F Hughes
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Leif D Jacobson
- Schrödinger, Inc., 101 SW Main St., Suite 1300, Portland, Oregon 97204, USA
| | - H Shaun Kwak
- Schrödinger, Inc., 101 SW Main St., Suite 1300, Portland, Oregon 97204, USA
| | - Daniel S Levine
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Daniel T Mainz
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Kevin B Moore
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Mats Svensson
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Pablo E Videla
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Mark A Watson
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Richard A Friesner
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, USA
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4
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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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5
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Ehrlich RS, Dasgupta S, Jessup RE, Teppang KL, Shiao AL, Jeoung KY, Su X, Shivkumar A, Theodorakis EA, Paesani F, Yang J. Excited State Rotational Freedom Impacts Viscosity Sensitivity in Arylcyanoamide Fluorescent Molecular Rotor Dyes. J Phys Chem B 2024; 128:3946-3952. [PMID: 38624216 DOI: 10.1021/acs.jpcb.4c00033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
The microviscosity of intracellular environments plays an important role in monitoring cellular function. Thus, the capability of detecting changes in viscosity can be utilized for the detection of different disease states. Viscosity-sensitive fluorescent molecular rotors are potentially excellent probes for these applications; however, the predictable relationships between chemical structural features and viscosity sensitivity are poorly understood. Here, we investigate a set of arylcyanoamide-based fluorescent probes and the effect of small aliphatic substituents on their viscosity sensitivity. We found that the location of the substituents and the type of π-network of the fluorophore can significantly affect the viscosity sensitivity of these fluorophores. Computational analysis supported the notion that the excited state rotational energy barrier plays a dominant role in the relative viscosity sensitivity of these fluorophores. These findings provide valuable insight into the design of molecular rotor-based fluorophores for viscosity measurement.
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Affiliation(s)
- Rachel S Ehrlich
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Saswata Dasgupta
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - R Erin Jessup
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Kristine L Teppang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Alexander L Shiao
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Kun Yong Jeoung
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Xuanmin Su
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Aashish Shivkumar
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Emmanuel A Theodorakis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Jerry Yang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
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6
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Sitkiewicz SP, Ferradás RR, Ramos-Cordoba E, Zaleśny R, Matito E, Luis JM. Spurious Oscillations Caused by Density Functional Approximations: Who is to Blame? Exchange or Correlation? J Chem Theory Comput 2024; 20:3144-3153. [PMID: 38570186 PMCID: PMC11044272 DOI: 10.1021/acs.jctc.3c01339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/05/2024]
Abstract
We analyze the varying susceptibilities of different density functional approximations (DFAs) to present spurious oscillations on the profiles of several vibrational properties. Among other problems, these spurious oscillations cause significant errors in harmonic and anharmonic IR and Raman frequencies and intensities. This work hinges on a judicious strategy to dissect the exchange and correlation components of DFAs and pinpoint the origins of these oscillations. We identify spurious oscillations in derivatives of all energy components with respect to nuclear displacements, including those energy terms that do not involve numerical integrations. These indirect spurious oscillations are attributed to suboptimal electron densities resulting from a self-consistent field procedure using a DFA that exhibits direct spurious oscillations. Direct oscillations stem from inaccurate numerical integration of the exchange and correlation energy density functionals. A thorough analysis of direct spurious oscillations reveals that only a handful of exchange and correlation components are insensitive to spurious oscillations, giving rise to three families of functionals, BH&H, LSDA, and BLYP. Among the functionals in these families, we encounter four widespread DFAs: BLYP, B3LYP, LC-BLYP, and CAM-B3LYP. Certain DFAs like PBE appear less sensitive to spurious oscillations due to compensatory cancellations between their energy components. Additionally, we found non-negligible but small oscillations in PBE and TPSS, which could be safely employed provided a sufficiently large integration grid is used in the calculations. These findings hint at the key components of current approximations to be improved and emphasize the necessity to develop accurate DFAs suitable for studying molecular spectroscopies.
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Affiliation(s)
- Sebastian P. Sitkiewicz
- Donostia
International Physics Center (DIPC), Donostia 20018, Euskadi, Spain
- Wrocław
Centre for Networking and Supercomputing, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, Wrocław PL-50370, Poland
| | - Rubén R. Ferradás
- Donostia
International Physics Center (DIPC), Donostia 20018, Euskadi, Spain
| | - Eloy Ramos-Cordoba
- Donostia
International Physics Center (DIPC), Donostia 20018, Euskadi, Spain
- Polimero
eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea,
Euskal Herriko Unibertsitatea UPV/EHU, P.K. 1072, Donostia 20080, Euskadi, Spain
- Ikerbasque
Foundation for Science, Plaza Euskadi 5, Bilbao 48009, Euskadi, Spain
- Institute
for Advanced Chemistry of Catalonia (IQAC), CSIC, Jordi Girona 18-26, Barcelona 08034, Spain
| | - Robert Zaleśny
- Faculty
of
Chemistry, Wrocław University of Science
and Technology, Wyb.
Wyspiańskiego 27, Wrocław PL-50370, Poland
| | - Eduard Matito
- Donostia
International Physics Center (DIPC), Donostia 20018, Euskadi, Spain
- Ikerbasque
Foundation for Science, Plaza Euskadi 5, Bilbao 48009, Euskadi, Spain
| | - Josep M. Luis
- Institut
de Química Computacional i Catàlisi (IQCC) and Departament
de Química, Universitat de Girona, Girona 17003, Catalonia, Spain
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7
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Dasgupta S, Palos E, Pan Y, Paesani F. Balance between Physical Interpretability and Energetic Predictability in Widely Used Dispersion-Corrected Density Functionals. J Chem Theory Comput 2024; 20:49-67. [PMID: 38150541 DOI: 10.1021/acs.jctc.3c00903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
We assess the performance of different dispersion models for several popular density functionals across a diverse set of noncovalent systems, ranging from the benzene dimer to molecular crystals. By analyzing the interaction energies and their individual components, we demonstrate that there exists variability across different systems for empirical dispersion models, which are calibrated for reproducing the interaction energies of specific systems. Thus, parameter fitting may undermine the underlying physics, as dispersion models rely on error compensation among the different components of the interaction energy. Energy decomposition analyses reveal that, the accuracy of revPBE-D3 for some aqueous systems originates from significant compensation between dispersion and charge transfer energies. However, revPBE-D3 is less accurate in describing systems where error compensation is incomplete, such as the benzene dimer. Such cases highlight the propensity for unpredictable behavior in various dispersion-corrected density functionals across a wide range of molecular systems, akin to the behavior of force fields. On the other hand, we find that SCAN-rVV10, a targeted-dispersion approach, affords significant reductions in errors associated with the lattice energies of molecular crystals, while it has limited accuracy in reproducing structural properties. Given the ubiquitous nature of noncovalent interactions and the key role of density functional theory in computational sciences, the future development of dispersion models should prioritize the faithful description of the dispersion energy, a shift that promises greater accuracy in capturing the underlying physics across diverse molecular and extended systems.
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Affiliation(s)
- Saswata Dasgupta
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Etienne Palos
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Yuanhui Pan
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
- Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, United States
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
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8
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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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9
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Wang Z, Liang J, Head-Gordon M. Earth Mover's Distance as a Metric to Evaluate the Extent of Charge Transfer in Excitations Using Discretized Real-Space Densities. J Chem Theory Comput 2023; 19:7704-7714. [PMID: 37922416 DOI: 10.1021/acs.jctc.3c00894] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2023]
Abstract
This paper presents a novel theoretical measure, μEMD, based on the earth mover's distance (EMD), for quantifying the density shift caused by electronic excitations in molecules. As input, the EMD metric uses only the discretized ground- and excited-state electron densities in real space, rendering it compatible with almost all electronic structure methods used to calculate excited states. The EMD metric is compared against other popular theoretical metrics for describing the extent of electron-hole separation in a wide range of excited states (valence, Rydberg, charge transfer, etc.). The results showcase the EMD metric's effectiveness across all excitation types and suggest that it is useful as an additional tool to characterize electronic excitations. The study also reveals that μEMD can function as a promising diagnostic tool for predicting the failure of pure exchange-correlation functionals. Specifically, we show statistical relationships among the functional-driven errors, the exact exchange content within the functional, and the magnitude of μEMD values.
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Affiliation(s)
- Zhe Wang
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
| | - Jiashu Liang
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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10
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Jana S, Herbert JM. Fractional-Electron and Transition-Potential Methods for Core-to-Valence Excitation Energies Using Density Functional Theory. J Chem Theory Comput 2023; 19:4100-4113. [PMID: 37312236 DOI: 10.1021/acs.jctc.3c00202] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Methods for computing X-ray absorption spectra based on a constrained core hole (possibly containing a fractional electron) are examined. These methods are based on Slater's transition concept and its generalizations, wherein core-to-valence excitation energies are determined using Kohn-Sham orbital energies. Methods examined here avoid promoting electrons beyond the lowest unoccupied molecular orbital, facilitating robust convergence. Variants of these ideas are systematically tested, revealing a best-case accuracy of 0.3-0.4 eV (with respect to experiment) for K-edge transition energies. Absolute errors are much larger for higher-lying near-edge transitions but can be reduced below 1 eV by introducing an empirical shift based on a charge-neutral transition-potential method, in conjunction with functionals such as SCAN, SCAN0, or B3LYP. This procedure affords an entire excitation spectrum from a single fractional-electron calculation, at the cost of ground-state density functional theory and without the need for state-by-state calculations. This shifted transition-potential approach may be especially useful for simulating transient spectroscopies or in complex systems where excited-state Kohn-Sham calculations are challenging.
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Affiliation(s)
- Subrata Jana
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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11
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Zhao F, Li Y, Houk KN, Lu Q, Liu F. Computational Elucidation on the Conformational Control of Selectivity in Intramolecular Ring-Closing Metathesis vs Intermolecular Homometathesis. J Org Chem 2023. [PMID: 37364253 DOI: 10.1021/acs.joc.3c00466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
The ring-closing metathesis reaction of diene plays an important role in the construction of cyclic compounds. In this research, density functional theory (DFT) calculations were conducted to elucidate the mechanisms and origins of the selectivity of ring-closing metathesis and homometathesis. The computational results suggest that the selectivity is determined by the substrate conformation. For the ester-tethered substrate, the homometathesis is more favorable, due to the planar structure of ester facilitating the conjugative effect of the formed E-homometathesis product. For the amide-tethered substrate, the ring-closing metathesis product is the only observed product because the steric hindrance of N-substituents disfavors homometathesis.
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Affiliation(s)
- Fengyue Zhao
- College of Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yixuan Li
- College of Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Qianqian Lu
- College of Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Fang Liu
- College of Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
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12
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Liang J, Feng X, Liu X, Head-Gordon M. Analytical harmonic vibrational frequencies with VV10-containing density functionals: Theory, efficient implementation, and benchmark assessments. J Chem Phys 2023; 158:204109. [PMID: 37218699 PMCID: PMC10208678 DOI: 10.1063/5.0152838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 04/27/2023] [Indexed: 05/24/2023] Open
Abstract
VV10 is a powerful nonlocal density functional for long-range correlation that is used to include dispersion effects in many modern density functionals, such as the meta-generalized gradient approximation (mGGA), B97M-V, the hybrid GGA, ωB97X-V, and the hybrid mGGA, ωB97M-V. While energies and analytical gradients for VV10 are already widely available, this study reports the first derivation and efficient implementation of the analytical second derivatives of the VV10 energy. The additional compute cost of the VV10 contributions to analytical frequencies is shown to be small in all but the smallest basis sets for recommended grid sizes. This study also reports the assessment of VV10-containing functionals for predicting harmonic frequencies using the analytical second derivative code. The contribution of VV10 to simulating harmonic frequencies is shown to be small for small molecules but important for systems where weak interactions are important, such as water clusters. In the latter cases, B97M-V, ωB97M-V, and ωB97X-V perform very well. The convergence of frequencies with respect to the grid size and atomic orbital basis set size is studied, and recommendations are reported. Finally, scaling factors to allow comparison of scaled harmonic frequencies with experimental fundamental frequencies and to predict zero-point vibrational energy are presented for some recently developed functionals (including r2SCAN, B97M-V, ωB97X-V, M06-SX, and ωB97M-V).
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Affiliation(s)
- Jiashu Liang
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, USA
| | | | - Xiao Liu
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, USA
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13
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Bowling PE, Broderick DR, Herbert JM. Fragment-Based Calculations of Enzymatic Thermochemistry Require Dielectric Boundary Conditions. J Phys Chem Lett 2023; 14:3826-3834. [PMID: 37061921 DOI: 10.1021/acs.jpclett.3c00533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Electronic structure calculations on enzymes require hundreds of atoms to obtain converged results, but fragment-based approximations offer a cost-effective solution. We present calculations on enzyme models containing 500-600 atoms using the many-body expansion, comparing to benchmarks in which the entire enzyme-substrate complex is described at the same level of density functional theory. When the amino acid fragments contain ionic side chains, the many-body expansion oscillates under vacuum boundary conditions but rapid convergence is restored using low-dielectric boundary conditions. This implies that full-system calculations in the gas phase are inappropriate benchmarks for assessing errors in fragment-based approximations. A three-body protocol retains sub-kilocalorie per mole fidelity with respect to a supersystem calculation, as does a two-body calculation combined with a full-system correction at a low-cost level of theory. These protocols pave the way for application of high-level quantum chemistry to large systems via rigorous, ab initio treatment of many-body polarization.
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Affiliation(s)
- Paige E Bowling
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Dustin R Broderick
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - John M Herbert
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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14
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Jana S, Herbert JM. Slater transition methods for core-level electron binding energies. J Chem Phys 2023; 158:094111. [PMID: 36889976 DOI: 10.1063/5.0134459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
Methods for computing core-level ionization energies using self-consistent field (SCF) calculations are evaluated and benchmarked. These include a "full core hole" (or "ΔSCF") approach that fully accounts for orbital relaxation upon ionization, but also methods based on Slater's transition concept in which the binding energy is estimated from an orbital energy level that is obtained from a fractional-occupancy SCF calculation. A generalization that uses two different fractional-occupancy SCF calculations is also considered. The best of the Slater-type methods afford mean errors of 0.3-0.4 eV with respect to experiment for a dataset of K-shell ionization energies, a level of accuracy that is competitive with more expensive many-body techniques. An empirical shifting procedure with one adjustable parameter reduces the average error below 0.2 eV. This shifted Slater transition method is a simple and practical way to compute core-level binding energies using only initial-state Kohn-Sham eigenvalues. It requires no more computational effort than ΔSCF and may be especially useful for simulating transient x-ray experiments where core-level spectroscopy is used to probe an excited electronic state, for which the ΔSCF approach requires a tedious state-by-state calculation of the spectrum. As an example, we use Slater-type methods to model x-ray emission spectroscopy.
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Affiliation(s)
- Subrata Jana
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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15
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Hesselmann A, Werner HJ, Knowles PJ. Thermochemical evaluation of adaptive and fixed density functional theory quadrature schemes. J Chem Phys 2022; 157:234106. [PMID: 36550055 DOI: 10.1063/5.0119622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
A systematic study is made of the accuracy and efficiency of a number of existing quadrature schemes for molecular Kohn-Sham Density-Functional Theory (DFT) using 408 molecules and 254 chemical reactions. Included are the fixed SG-x (x = 0-3) grids of Gill et al., Dasgupta, and Herbert, the 3-zone grids of Treutler and Ahlrichs, a fixed five-zone grid implemented in Molpro, and a new adaptive grid scheme. While all methods provide a systematic reduction of errors upon extension of the grid sizes, significant differences are observed in the accuracies for similar grid sizes with various approaches. For the tests in this work, the SG-x fixed grids are less suitable to achieve high accuracies in the DFT integration, while our new adaptive grid performed best among the schemes studied in this work. The extra computational time to generate the adaptive grid scales linearly with molecular size and is negligible compared with the time needed for the self-consistent field iterations for large molecules. A comparison of the grid accuracies using various density functionals shows that meta-GGA functionals need larger integration grids than GGA functionals to reach the same degree of accuracy, confirming previous investigations of the numerical stability of meta-GGA functionals. On the other hand, the grid integration errors are almost independent of the basis set, and the basis set errors are mostly much larger than the errors caused by the numerical integrations, even when using the smallest grids tested in this work.
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Affiliation(s)
- Andreas Hesselmann
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Hans-Joachim Werner
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Peter J Knowles
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
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16
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Gray M, Bowling PE, Herbert JM. Systematic Evaluation of Counterpoise Correction in Density Functional Theory. J Chem Theory Comput 2022; 18:6742-6756. [PMID: 36251499 DOI: 10.1021/acs.jctc.2c00883] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A widespread belief persists that the Boys-Bernardi function counterpoise (CP) procedure "overcorrects" supramolecular interaction energies for the effects of basis-set superposition error. To the extent that this is true for correlated wave function methods, it is usually an artifact of low-quality basis sets. The question has not been considered systematically in the context of density functional theory, however, where basis-set convergence is generally less problematic. We present a systematic assessment of the CP procedure for a representative set of functionals and basis sets, considering both benchmark data sets of small dimers and larger supramolecular complexes. The latter include layered composite polymers with ∼150 atoms and ligand-protein models with ∼300 atoms. Provided that CP correction is used, we find that intermolecular interaction energies of nearly complete-basis quality can be obtained using only double-ζ basis sets. This is less expensive as compared to triple-ζ basis sets without CP correction. CP-corrected interaction energies are less sensitive to the presence of diffuse basis functions as compared to uncorrected energies, which is important because diffuse functions are expensive and often numerically problematic for large systems. Our results upend the conventional wisdom that CP "overcorrects" for basis-set incompleteness. In small basis sets, CP correction is mandatory in order to demonstrate that the results do not rest on error cancellation.
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Affiliation(s)
- Montgomery Gray
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio43210, United States
| | - Paige E Bowling
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio43210, United States.,Biophysics Graduate Program, The Ohio State University, Columbus, Ohio43210, United States
| | - John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio43210, United States.,Biophysics Graduate Program, The Ohio State University, Columbus, Ohio43210, United States
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17
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Reese DL, Steele RP. Molecular Motion in the Interconverting σ-H 2, Di-, and Tri-hydride Regimes: Mo(PH3)5H2. J Phys Chem A 2022; 126:6834-6848. [PMID: 36154020 DOI: 10.1021/acs.jpca.2c03397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The transition-metal complex Mo(PH3)5H2 is known to exist in three possible isomeric forms, including a nonclassical, σ-bound dihydrogen complex and two classical dihydride isomers. As such, it has served as a model complex for the energies of conversion between these limiting structural regimes. In the present study, ab initio molecular dynamics computer simulations, combined with enhanced sampling techniques, were utilized to directly assess the degree of motion and isomerization of the dihydrogen/dihydride moieties in this complex. Ligand rotations (for both the H2 unit and the phosphine units) were found to be dominant in the low-temperature (298 K) regime, and the classical thermodynamic distribution showed no probability of thermally accessing dihydride forms, although unrestrained molecular dynamics trajectories showed fleeting configurations outside of the σ-H2 configuration. Simulations at higher temperatures surprisingly revealed new tri-hydride isomers that are energetically competitive with the σ-H2 and cis-/trans-dihydride isomers. Low-energy pathways to hydrogen/hydride transfer and phosphine dissociation were readily accessible, which considerably expands the known isomeric flexibility of this complex.
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Affiliation(s)
- Diana L Reese
- Department of Chemistry and Biochemistry, Utah Tech University, 225 South University Avenue, St. George, Utah 84770, 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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18
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Satalkar V, Benassi E, Mao Y, Pan X, Ran C, Chen X, Shao Y. Computational Investigation of Substituent Effects on the Fluorescence Wavelengths of Oxyluciferin Analogs. J Photochem Photobiol A Chem 2022; 431:114018. [PMID: 36407037 PMCID: PMC9673899 DOI: 10.1016/j.jphotochem.2022.114018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Oxyluciferin, which is the light emitter for firefly bioluminescence, has been subjected to extensive chemical modifications to tune its emission wavelength and quantum yield. However, the exact mechanisms for various electron-donating and withdrawing groups to perturb the photophysical properties of oxyluciferin analogs are still not fully understood. To elucidate the substituent effects on the fluorescence wavelength of oxyluciferin analogs, we applied the absolutely localized molecular orbitals (ALMO)-based frontier orbital analysis to assess various types of interactions (i.e. permanent electrostatics/exchange repulsion, polarization, occupied-occupied orbital mixing, virtual-virtual orbital mixing, and charge-transfer) between the oxyluciferin and substituent orbitals. We suggested two distinct mechanisms that can lead to red-shifted oxyluciferin emission wavelength, a design objective that can help increase the tissue penetration of bioluminescence emission. Within the first mechanism, an electron-donating group (such as an amino or dimethylamino group) can contribute its highest occupied molecular orbital (HOMO) to an out-of-phase combination with oxyluciferin's HOMO, thus raising the HOMO energy of the substituted analog and narrowing its HOMO-LUMO gap. Alternatively, an electron-withdrawing group (such as a nitro or cyano group) can participate in an in-phase virtual-virtual orbital mixing of fragment LUMOs, thus lowering the LUMO energy of the substituted analog. Such an ALMO-based frontier orbital analysis is expected to lead to intuitive principles for designing analogs of not only the oxyluciferin molecule, but also many other functional dyes.
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Affiliation(s)
- Vardhan Satalkar
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Enrico Benassi
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Yuezhi Mao
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Xiaoliang Pan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Chongzhao Ran
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Charlestown, Boston, MA 02129, USA
| | - Xiaoyuan Chen
- Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, 117597, Singapore
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
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19
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Hanson-Heine MWD. Metal sandwich and ion complexes in cyclacene nanobelts. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2118187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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20
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Santra G, Calinsky R, Martin JML. Benefits of Range-Separated Hybrid and Double-Hybrid Functionals for a Large and Diverse Data Set of Reaction Energies and Barrier Heights. J Phys Chem A 2022; 126:5492-5505. [PMID: 35930677 PMCID: PMC9393870 DOI: 10.1021/acs.jpca.2c03922] [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: 11/28/2022]
Abstract
![]()
To better understand the thermochemical kinetics and
mechanism
of a specific chemical reaction, an accurate estimation of barrier
heights (forward and reverse) and reaction energies is vital. Because
of the large size of reactants and transition state structures involved
in real-life mechanistic studies (e.g., enzymatically catalyzed reactions),
density functional theory remains the workhorse for such calculations.
In this paper, we have assessed the performance of 91 density functionals
for modeling the reaction energies and barrier heights on a large
and chemically diverse data set (BH9) composed of 449 organic chemistry
reactions. We have shown that range-separated hybrid functionals perform
better than the global hybrids for BH9 barrier heights and reaction
energies. Except for the PBE-based range-separated nonempirical double
hybrids, range separation of the exchange term helps improve the performance
for barrier heights and reaction energies. The 16-parameter Berkeley
double hybrid, ωB97M(2), performs remarkably well for both properties.
However, our minimally empirical range-separated double hybrid functionals
offer marginally better accuracy than ωB97M(2) for BH9 barrier
heights and reaction energies.
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Affiliation(s)
- Golokesh Santra
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Reḥovot, Israel
| | - Rivka Calinsky
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Reḥovot, Israel
| | - Jan M L Martin
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Reḥovot, Israel
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21
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Sparrow ZM, Ernst BG, Quady TK, DiStasio RA. Uniting Nonempirical and Empirical Density Functional Approximation Strategies Using Constraint-Based Regularization. J Phys Chem Lett 2022; 13:6896-6904. [PMID: 35863751 DOI: 10.1021/acs.jpclett.2c00643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In this work, we present a general framework that unites the two primary strategies for constructing density functional approximations (DFAs): nonempirical (NE) constraint satisfaction and empirical (E) data-driven optimization. The proposed method employs B-splines, bell-shaped spline functions with compact support, to construct each inhomogeneity correction factor (ICF). This choice offers several distinct advantages over traditional polynomial expansions by enabling explicit enforcement of linear and nonlinear constraints as well as ICF smoothness using Tikhonov and penalized B-splines (P-splines) regularization. As proof-of-concept, we use the so-called CASE (constrained and smoothed empirical) framework to construct a constraint-satisfying and data-driven global hybrid that exhibits enhanced performance across a diverse set of chemical properties. We argue that the CASE approach can be used to generate DFAs that maintain the physical rigor and transferability of NE-DFAs while leveraging high-quality quantum-mechanical data to remove the arbitrariness of ansatz selection and improve performance.
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Affiliation(s)
- Zachary M Sparrow
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Brian G Ernst
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Trine K Quady
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Robert A DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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22
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Dasgupta S, Shahi C, Bhetwal P, Perdew JP, Paesani F. How Good Is the Density-Corrected SCAN Functional for Neutral and Ionic Aqueous Systems, and What Is So Right about the Hartree-Fock Density? J Chem Theory Comput 2022; 18:4745-4761. [PMID: 35785808 DOI: 10.1021/acs.jctc.2c00313] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Density functional theory (DFT) is the most widely used electronic structure method, due to its simplicity and cost effectiveness. The accuracy of a DFT calculation depends not only on the choice of the density functional approximation (DFA) adopted but also on the electron density produced by the DFA. SCAN is a modern functional that satisfies all known constraints for meta-GGA functionals. The density-driven errors, defined as energy errors arising from errors of the self-consistent DFA electron density, can hinder SCAN from achieving chemical accuracy in some systems, including water. Density-corrected DFT (DC-DFT) can alleviate this shortcoming by adopting a more accurate electron density which, in most applications, is the electron density obtained at the Hartree-Fock level of theory due to its relatively low computational cost. In this work, we present extensive calculations aimed at determining the accuracy of the DC-SCAN functional for various aqueous systems. DC-SCAN (SCAN@HF) shows remarkable consistency in reproducing reference data obtained at the coupled cluster level of theory, with minimal loss of accuracy. Density-driven errors in the description of ionic aqueous clusters are thoroughly investigated. By comparison with the orbital-optimized CCD density in the water dimer, we find that the self-consistent SCAN density transfers a spurious fraction of an electron across the hydrogen bond to the hydrogen atom (H*, covalently bound to the donor oxygen atom) from the acceptor (OA) and donor (OD) oxygen atoms, while HF makes a much smaller spurious transfer in the opposite direction, consistent with DC-SCAN (SCAN@HF) reduction of SCAN overbinding due to delocalization error. While LDA seems to be the conventional extreme of density delocalization error, and HF the conventional extreme of (usually much smaller) density localization error, these two densities do not quite yield the conventional range of density-driven error in energy differences. Finally, comparisons of the DC-SCAN results with those obtained with the Fermi-Löwdin orbital self-interaction correction (FLOSIC) method show that DC-SCAN represents a more accurate approach to reducing density-driven errors in SCAN calculations of ionic aqueous clusters. While the HF density is superior to that of SCAN for noncompact water clusters, the opposite is true for the compact water molecule with exactly 10 electrons.
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Affiliation(s)
- Saswata Dasgupta
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Chandra Shahi
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Pradeep Bhetwal
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - John P Perdew
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States.,Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States.,Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, United States.,San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
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23
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Sitkiewicz S, Zaleśny R, Ramos-Cordoba E, Luis JM, Matito E. How Reliable Are Modern Density Functional Approximations to Simulate Vibrational Spectroscopies? J Phys Chem Lett 2022; 13:5963-5968. [PMID: 35735354 PMCID: PMC9251762 DOI: 10.1021/acs.jpclett.2c01278] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We show that properties of molecules with low-frequency modes calculated with density functional approximations (DFAs) suffer from spurious oscillations along the nuclear displacement coordinate due to numerical integration errors. Occasionally, the problem can be alleviated using extensive integration grids that compromise the favorable cost-accuracy ratio of DFAs. Since spurious oscillations are difficult to predict or identify, DFAs are exposed to severe performance errors in IR and Raman intensities and frequencies or vibrational contributions to any molecular property. Using Fourier spectral analysis and digital signal processing techniques, we identify and quantify the error due to these oscillations for 45 widely used DFAs. LC-BLYP and BH&H are revealed as the only functionals showing robustness against the spurious oscillations of various energy, dipole moment, and polarizability derivatives with respect to a nuclear displacement coordinate. Given the ubiquitous nature of molecules with low-frequency modes, we warrant caution in using modern DFAs to simulate vibrational spectroscopies.
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Affiliation(s)
- Sebastian
P. Sitkiewicz
- Donostia
International Physics Center (DIPC), 20018 Donostia, Euskadi, Spain
- Polimero
eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU, P.K. 1072, 20080 Donostia, Euskadi, Spain
| | - Robert Zaleśny
- Faculty
of Chemistry, Wrocław University of
Science and Technology, Wyb. Wyspiańskiego 27, PL−50370 Wrocław, Poland
| | - Eloy Ramos-Cordoba
- Donostia
International Physics Center (DIPC), 20018 Donostia, Euskadi, Spain
- Polimero
eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU, P.K. 1072, 20080 Donostia, Euskadi, Spain
| | - Josep M. Luis
- Institut
de Química Computacional i Catàlisi (IQCC) and Departament
de Química, Universitat de Girona, 17003 Girona, Catalonia, Spain
| | - Eduard Matito
- Donostia
International Physics Center (DIPC), 20018 Donostia, Euskadi, Spain
- Ikerbasque
Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Euskadi, Spain
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24
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Zhu Y, Herbert JM. High harmonic spectra computed using time-dependent Kohn-Sham theory with Gaussian orbitals and a complex absorbing potential. J Chem Phys 2022; 156:204123. [PMID: 35649850 DOI: 10.1063/5.0079910] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
High harmonic spectra for H2 and H2 + are simulated by solving the time-dependent Kohn-Sham equation in the presence of a strong laser field using an atom-centered Gaussian representation of the density and a complex absorbing potential. The latter serves to mitigate artifacts associated with the finite extent of the basis functions, including spurious reflection of the outgoing electronic wave packet. Interference between the outgoing and reflected waves manifests as peak broadening in the spectrum as well as the appearance of spurious high-energy peaks after the harmonic progression has terminated. We demonstrate that well-resolved spectra can be obtained through the use of an atom-centered absorbing potential. As compared to grid-based algorithms, the present approach is more readily extensible to larger molecules.
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Affiliation(s)
- Ying Zhu
- Department of Chemistry and Biochemistry, and Chemical Physics Graduate Program, The Ohio State University, Columbus, Ohio 43210, USA
| | - John M Herbert
- Department of Chemistry and Biochemistry, and Chemical Physics Graduate Program, The Ohio State University, Columbus, Ohio 43210, USA
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25
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Palos E, Lambros E, Swee S, Hu J, Dasgupta S, Paesani F. Assessing the Interplay between Functional-Driven and Density-Driven Errors in DFT Models of Water. J Chem Theory Comput 2022; 18:3410-3426. [PMID: 35506889 DOI: 10.1021/acs.jctc.2c00050] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigate the interplay between functional-driven and density-driven errors in different density functional approximations within density functional theory (DFT) and the implications of these errors for simulations of water with DFT-based data-driven potentials. Specifically, we quantify density-driven errors in two widely used dispersion-corrected functionals derived within the generalized gradient approximation (GGA), namely BLYP-D3 and revPBE-D3, and two modern meta-GGA functionals, namely strongly constrained and appropriately normed (SCAN) and B97M-rV. The effects of functional-driven and density-driven errors on the interaction energies are first assessed for the water clusters of the BEGDB dataset. Further insights into the nature of functional-driven errors are gained from applying the absolutely localized molecular orbital energy decomposition analysis (ALMO-EDA) to the interaction energies, which demonstrates that functional-driven errors are strongly correlated with the nature of the interactions. We discuss cases where density-corrected DFT (DC-DFT) models display higher accuracy than the original DFT models and cases where reducing the density-driven errors leads to larger deviations from the reference energies due to the presence of large functional-driven errors. Finally, molecular dynamics simulations are performed with data-driven many-body potentials derived from DFT and DC-DFT data to determine the effect that minimizing density-driven errors has on the description of liquid water. Besides rationalizing the performance of widely used DFT models of water, we believe that our findings unveil fundamental relations between the shortcomings of some common DFT approximations and the requirements for accurate descriptions of molecular interactions, which will aid the development of a consistent, DFT-based framework for the development of data-driven and machine-learned potentials for simulations of condensed-phase systems.
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Affiliation(s)
- Etienne Palos
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Eleftherios Lambros
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Steven Swee
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Jie Hu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Saswata Dasgupta
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States.,Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, United States.,San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
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26
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Santra G, Martin JML. Do Double-Hybrid Functionals Benefit from Regularization in the PT2 Term? Observations from an Extensive Benchmark. J Phys Chem Lett 2022; 13:3499-3506. [PMID: 35417181 PMCID: PMC9036584 DOI: 10.1021/acs.jpclett.2c00718] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
We put to the test a recent suggestion [Shee, J., et al. J. Phys. Chem. Lett. 2021, 12 (50), 12084-12097] that MP2 regularization might improve the performance of double-hybrid density functionals. Using the very large and chemically diverse GMTKN55 benchmark, we find that κ-regularization is indeed beneficial at lower percentages of Hartree-Fock exchange, especially if spin-component scaling is not applied [such as in B2GP-PLYP or ωB97M(2)]. This benefit dwindles for DSD and DOD functionals and vanishes entirely in the ∼70% HF exchange region optimal for them.
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27
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Chodkiewicz M, Pawlędzio S, Woińska M, Woźniak K. Fragmentation and transferability in Hirshfeld atom refinement. IUCRJ 2022; 9:298-315. [PMID: 35371499 PMCID: PMC8895009 DOI: 10.1107/s2052252522000690] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/19/2022] [Indexed: 05/06/2023]
Abstract
Hirshfeld atom refinement (HAR) is one of the most effective methods for obtaining accurate structural parameters for hydrogen atoms from X-ray diffraction data. Unfortunately, it is also relatively computationally expensive, especially for larger molecules due to wavefunction calculations. Here, a fragmentation approach has been tested as a remedy for this problem. It gives an order of magnitude improvement in computation time for larger organic systems and is a few times faster for metal-organic systems at the cost of only minor differences in the calculated structural parameters when compared with the original HAR calculations. Fragmentation was also applied to polymeric and disordered systems where it provides a natural solution to problems that arise when HAR is applied. The concept of fragmentation is closely related to the transferable aspherical atom model (TAAM) and allows insight into possible ways to improve TAAM. Hybrid approaches combining fragmentation with the transfer of atomic densities between chemically similar atoms have been tested. An efficient handling of intermolecular interactions was also introduced for calculations involving fragmentation. When applied in fragHAR (a fragmentation approach for polypeptides) as a replacement for the original approach, it allowed for more efficient calculations. All of the calculations were performed with a locally modified version of Olex2 combined with a development version of discamb2tsc and ORCA. Care was taken to efficiently use the power of multicore processors by simple implementation of load-balancing, which was found to be very important for lowering computational time.
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Affiliation(s)
- Michał Chodkiewicz
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland
- Correspondence e-mail: ,
| | - Sylwia Pawlędzio
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland
| | - Magdalena Woińska
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland
- Correspondence e-mail: ,
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28
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Ashraf A, Herbert JM, Muhammad S, Farooqi BA, Farooq U, Salman M, Ayub K. Theoretical Approach to Evaluate the Gas-Sensing Performance of Graphene Nanoribbon/Oligothiophene Composites. ACS OMEGA 2022; 7:2260-2274. [PMID: 35071915 PMCID: PMC8772315 DOI: 10.1021/acsomega.1c05863] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Composite formation with graphene is an effective approach to increase the sensitivity of polythiophene (nPT) gas sensors. The interaction mechanism between gaseous analytes and graphene/nPT composite systems is still not clear, and density functional theory calculations are used to explore the interaction mechanism between graphene/nPT nanoribbon composites (with n = 3-9 thiophene units) and gaseous analytes CO, NH3, SO2, and NO2. For the studied analytes, the interaction energy ranges from -44.28 kcal/mol for (C54H30-3PT)-NO2 to -2.37 kcal/mol for (C54H30-3PT)-CO at the counterpoise-corrected ωB97M-V/def2-TZVPD level of theory. The sensing mechanism is further evaluated by geometric analysis, ultraviolet-visible spectroscopy, density of-states analysis, calculation of global reactivity indices, and both frontier and natural bond orbital analyses. The variation in the highest occupied molecular orbital/lowest unoccupied molecular orbital gap of the composite indicates the change in conductivity upon complexation with the analyte. Energy decomposition analysis reveals that dispersion and charge transfer make the largest contributions to the interaction energy. The graphene/oligothiophene composite is more sensitive toward these analytes than either component taken alone due to larger changes in the orbital gap. The computational framework established in the present work can be used to evaluate and design graphene/nPT nanoribbon composite materials for gas sensors.
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Affiliation(s)
- Ayesha Ashraf
- Department
of Chemistry and Biochemistry, The Ohio
State University, Columbus, Ohio 43210, USA
| | - John M. Herbert
- Department
of Chemistry and Biochemistry, The Ohio
State University, Columbus, Ohio 43210, USA
| | - Shabbir Muhammad
- Department
of Physics, College of Science, King Khalid
University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Bilal Ahmad Farooqi
- Institute
of Chemistry, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590 Pakistan
| | - Umar Farooq
- Institute
of Chemistry, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590 Pakistan
| | - Muhammad Salman
- Institute
of Chemistry, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590 Pakistan
| | - Khurshid Ayub
- Department
of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
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29
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Zech A, Head-Gordon M. Dissociation of HCl in water nanoclusters: an energy decomposition analysis perspective. Phys Chem Chem Phys 2021; 23:26737-26749. [PMID: 34846396 DOI: 10.1039/d1cp04587c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
As known, small HCl-water nanoclusters display a particular dissociation behaviour, whereby at least four water molecules are required for the ionic dissociation of HCl. In this work, we examine how intermolecular interactions promote the ionic dissociation of such nanoclusters. To this end, a set of 45 HCl-water nanoclusters with up to four water molecules is introduced. Energy decomposition analysis based on absolutely localized molecular orbitals (ALMO-EDA) is employed in order to study the importance of frozen interaction, dispersion, polarization, and charge-transfer for the dissociation. The vertical ALMO-EDA scheme is applied to HCl-water clusters along a proton-transfer coordinate varying the amount of spectator water molecules. The corresponding ALMO-EDA results show a clear preference for the dissociated cluster only in the presence of four water molecules. Our analysis of adiabatic ALMO-EDA results reveals a push-pull mechanism for the destabilization of the HCl bond based on the synergy between forward and backward charge-transfer.
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Affiliation(s)
- Alexander Zech
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA.
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA. .,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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30
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Herbert JM, Paul SK. Interaction Energy Analysis of Monovalent Inorganic Anions in Bulk Water Versus Air/Water Interface. Molecules 2021; 26:6719. [PMID: 34771133 PMCID: PMC8588468 DOI: 10.3390/molecules26216719] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 10/29/2021] [Accepted: 11/03/2021] [Indexed: 11/16/2022] Open
Abstract
Soft anions exhibit surface activity at the air/water interface that can be probed using surface-sensitive vibrational spectroscopy, but the structural implications of this surface activity remain a matter of debate. Here, we examine the nature of anion-water interactions at the air/water interface using a combination of molecular dynamics simulations and quantum-mechanical energy decomposition analysis based on symmetry-adapted perturbation theory. Results are presented for a set of monovalent anions, including Cl-, Br-, I-, CN-, OCN-, SCN-, NO2-, NO3-, and ClOn- (n=1,2,3,4), several of which are archetypal examples of surface-active species. In all cases, we find that average anion-water interaction energies are systematically larger in bulk water although the difference (with respect to the same quantity computed in the interfacial environment) is well within the magnitude of the instantaneous fluctuations. Specifically for the surface-active species Br-(aq), I-(aq), ClO4-(aq), and SCN-(aq), and also for ClO-(aq), the charge-transfer (CT) energy is found to be larger at the interface than it is in bulk water, by an amount that is greater than the standard deviation of the fluctuations. The Cl-(aq) ion has a slightly larger CT energy at the interface, but NO3-(aq) does not; these two species are borderline cases where consensus is lacking regarding their surface activity. However, CT stabilization amounts to <20% of the total induction energy for each of the ions considered here, and CT-free polarization energies are systematically larger in bulk water in all cases. As such, the role of these effects in the surface activity of soft anions remains unclear. This analysis complements our recent work suggesting that the short-range solvation structure around these ions is scarcely different at the air/water interface from what it is in bulk water. Together, these observations suggest that changes in first-shell hydration structure around soft anions cannot explain observed surface activities.
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Affiliation(s)
- John M. Herbert
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH 43210, USA;
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31
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Dasgupta S, Lambros E, Perdew JP, Paesani F. Elevating density functional theory to chemical accuracy for water simulations through a density-corrected many-body formalism. Nat Commun 2021; 12:6359. [PMID: 34737311 PMCID: PMC8569147 DOI: 10.1038/s41467-021-26618-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/08/2021] [Indexed: 11/09/2022] Open
Abstract
Density functional theory (DFT) has been extensively used to model the properties of water. Albeit maintaining a good balance between accuracy and efficiency, no density functional has so far achieved the degree of accuracy necessary to correctly predict the properties of water across the entire phase diagram. Here, we present density-corrected SCAN (DC-SCAN) calculations for water which, minimizing density-driven errors, elevate the accuracy of the SCAN functional to that of "gold standard" coupled-cluster theory. Building upon the accuracy of DC-SCAN within a many-body formalism, we introduce a data-driven many-body potential energy function, MB-SCAN(DC), that quantitatively reproduces coupled cluster reference values for interaction, binding, and individual many-body energies of water clusters. Importantly, molecular dynamics simulations carried out with MB-SCAN(DC) also reproduce the properties of liquid water, which thus demonstrates that MB-SCAN(DC) is effectively the first DFT-based model that correctly describes water from the gas to the liquid phase.
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Affiliation(s)
- Saswata Dasgupta
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Eleftherios Lambros
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - John P Perdew
- Department of Physics, Temple University, Philadelphia, PA, 19122, USA
- Department of Chemistry, Temple University, Philadelphia, PA, 19122, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA.
- Materials Science and Engineering, University of California, San Diego, La Jolla, CA, 92093, USA.
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, 92093, USA.
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32
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Kasim MF, Vinko SM. Learning the Exchange-Correlation Functional from Nature with Fully Differentiable Density Functional Theory. PHYSICAL REVIEW LETTERS 2021; 127:126403. [PMID: 34597107 DOI: 10.1103/physrevlett.127.126403] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
Improving the predictive capability of molecular properties in ab initio simulations is essential for advanced material discovery. Despite recent progress making use of machine learning, utilizing deep neural networks to improve quantum chemistry modeling remains severely limited by the scarcity and heterogeneity of appropriate experimental data. Here we show how training a neural network to replace the exchange-correlation functional within a fully differentiable three-dimensional Kohn-Sham density functional theory framework can greatly improve simulation accuracy. Using only eight experimental data points on diatomic molecules, our trained exchange-correlation networks enable improved prediction accuracy of atomization energies across a collection of 104 molecules containing new bonds, and atoms, that are not present in the training dataset.
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Affiliation(s)
- M F Kasim
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
| | - S M Vinko
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
- Central Laser Facility, STFC Rutherford Appleton Laboratory, Didcot OX11 0QX, United Kingdom
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33
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Lambros E, Dasgupta S, Palos E, Swee S, Hu J, Paesani F. General Many-Body Framework for Data-Driven Potentials with Arbitrary Quantum Mechanical Accuracy: Water as a Case Study. J Chem Theory Comput 2021; 17:5635-5650. [PMID: 34370954 DOI: 10.1021/acs.jctc.1c00541] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a general framework for the development of data-driven many-body (MB) potential energy functions (MB-QM PEFs) that represent the interactions between small molecules at an arbitrary quantum-mechanical (QM) level of theory. As a demonstration, a family of MB-QM PEFs for water is rigorously derived from density functionals belonging to different rungs across Jacob's ladder of approximations within density functional theory (MB-DFT) and from Møller-Plesset perturbation theory (MB-MP2). Through a systematic analysis of individual MB contributions to the interaction energies of water clusters, we demonstrate that all MB-QM PEFs preserve the same accuracy as the corresponding ab initio calculations, with the exception of those derived from density functionals within the generalized gradient approximation (GGA). The differences between the DFT and MB-DFT results are traced back to density-driven errors that prevent GGA functionals from accurately representing the underlying molecular interactions for different cluster sizes and hydrogen-bonding arrangements. We show that this shortcoming may be overcome, within the MB formalism, by using density-corrected functionals (DC-DFT) that provide a more consistent representation of each individual MB contribution. This is demonstrated through the development of a MB-DFT PEF derived from DC-PBE-D3 data, which more accurately reproduce the corresponding ab initio results.
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Affiliation(s)
- Eleftherios Lambros
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Saswata Dasgupta
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Etienne Palos
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Steven Swee
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Jie Hu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States.,Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, United States.,San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
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34
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Epifanovsky E, Gilbert ATB, Feng X, Lee J, Mao Y, Mardirossian N, Pokhilko P, White AF, Coons MP, Dempwolff AL, Gan Z, Hait D, Horn PR, Jacobson LD, Kaliman I, Kussmann J, Lange AW, Lao KU, Levine DS, Liu J, McKenzie SC, Morrison AF, Nanda KD, Plasser F, Rehn DR, Vidal ML, You ZQ, Zhu Y, Alam B, Albrecht BJ, Aldossary A, Alguire E, Andersen JH, Athavale V, Barton D, Begam K, Behn A, Bellonzi N, Bernard YA, Berquist EJ, Burton HGA, Carreras A, Carter-Fenk K, Chakraborty R, Chien AD, Closser KD, Cofer-Shabica V, Dasgupta S, de Wergifosse M, Deng J, Diedenhofen M, Do H, Ehlert S, Fang PT, Fatehi S, Feng Q, Friedhoff T, Gayvert J, Ge Q, Gidofalvi G, Goldey M, Gomes J, González-Espinoza CE, Gulania S, Gunina AO, Hanson-Heine MWD, Harbach PHP, Hauser A, Herbst MF, Hernández Vera M, Hodecker M, Holden ZC, Houck S, Huang X, Hui K, Huynh BC, Ivanov M, Jász Á, Ji H, Jiang H, Kaduk B, Kähler S, Khistyaev K, Kim J, Kis G, Klunzinger P, Koczor-Benda Z, Koh JH, Kosenkov D, Koulias L, Kowalczyk T, Krauter CM, Kue K, Kunitsa A, Kus T, Ladjánszki I, Landau A, Lawler KV, Lefrancois D, Lehtola S, Li RR, Li YP, Liang J, Liebenthal M, Lin HH, Lin YS, Liu F, Liu KY, Loipersberger M, Luenser A, Manjanath A, Manohar P, Mansoor E, Manzer SF, Mao SP, Marenich AV, Markovich T, Mason S, Maurer SA, McLaughlin PF, Menger MFSJ, Mewes JM, Mewes SA, Morgante P, Mullinax JW, Oosterbaan KJ, Paran G, Paul AC, Paul SK, Pavošević F, Pei Z, Prager S, Proynov EI, Rák Á, Ramos-Cordoba E, Rana B, Rask AE, Rettig A, Richard RM, Rob F, Rossomme E, Scheele T, Scheurer M, Schneider M, Sergueev N, Sharada SM, Skomorowski W, Small DW, Stein CJ, Su YC, Sundstrom EJ, Tao Z, Thirman J, Tornai GJ, Tsuchimochi T, Tubman NM, Veccham SP, Vydrov O, Wenzel J, Witte J, Yamada A, Yao K, Yeganeh S, Yost SR, Zech A, Zhang IY, Zhang X, Zhang Y, Zuev D, Aspuru-Guzik A, Bell AT, Besley NA, Bravaya KB, Brooks BR, Casanova D, Chai JD, Coriani S, Cramer CJ, Cserey G, DePrince AE, DiStasio RA, Dreuw A, Dunietz BD, Furlani TR, Goddard WA, Hammes-Schiffer S, Head-Gordon T, Hehre WJ, Hsu CP, Jagau TC, Jung Y, Klamt A, Kong J, Lambrecht DS, Liang W, Mayhall NJ, McCurdy CW, Neaton JB, Ochsenfeld C, Parkhill JA, Peverati R, Rassolov VA, Shao Y, Slipchenko LV, Stauch T, Steele RP, Subotnik JE, Thom AJW, Tkatchenko A, Truhlar DG, Van Voorhis T, Wesolowski TA, Whaley KB, Woodcock HL, Zimmerman PM, Faraji S, Gill PMW, Head-Gordon M, Herbert JM, Krylov AI. Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package. J Chem Phys 2021; 155:084801. [PMID: 34470363 PMCID: PMC9984241 DOI: 10.1063/5.0055522] [Citation(s) in RCA: 466] [Impact Index Per Article: 155.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange-correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear-electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an "open teamware" model and an increasingly modular design.
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Affiliation(s)
- Evgeny Epifanovsky
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | | | | | - Joonho Lee
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Yuezhi Mao
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Pavel Pokhilko
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Alec F. White
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Marc P. Coons
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Adrian L. Dempwolff
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Zhengting Gan
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Diptarka Hait
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Paul R. Horn
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Leif D. Jacobson
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | | | - Jörg Kussmann
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Adrian W. Lange
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Ka Un Lao
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Daniel S. Levine
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Simon C. McKenzie
- Research School of Chemistry, Australian National University, Canberra, Australia
| | | | - Kaushik D. Nanda
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Dirk R. Rehn
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Marta L. Vidal
- Department of Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kgs Lyngby, Denmark
| | | | - Ying Zhu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Bushra Alam
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Benjamin J. Albrecht
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | | | - Ethan Alguire
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Josefine H. Andersen
- Department of Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kgs Lyngby, Denmark
| | - Vishikh Athavale
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Dennis Barton
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Khadiza Begam
- Department of Physics, Kent State University, Kent, Ohio 44242, USA
| | - Andrew Behn
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Nicole Bellonzi
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Yves A. Bernard
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Hugh G. A. Burton
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Abel Carreras
- Donostia International Physics Center, 20080 Donostia, Euskadi, Spain
| | - Kevin Carter-Fenk
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | | | - Alan D. Chien
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - Vale Cofer-Shabica
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Saswata Dasgupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Marc de Wergifosse
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Jia Deng
- Research School of Chemistry, Australian National University, Canberra, Australia
| | | | - Hainam Do
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Sebastian Ehlert
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Beringstr. 4, 53115 Bonn, Germany
| | - Po-Tung Fang
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | | | - Qingguo Feng
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Triet Friedhoff
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - James Gayvert
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Qinghui Ge
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Gergely Gidofalvi
- Department of Chemistry and Biochemistry, Gonzaga University, Spokane, Washington 99258, USA
| | - Matthew Goldey
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Joe Gomes
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Sahil Gulania
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Anastasia O. Gunina
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Phillip H. P. Harbach
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Andreas Hauser
- Institute of Experimental Physics, Graz University of Technology, Graz, Austria
| | | | - Mario Hernández Vera
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Manuel Hodecker
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Zachary C. Holden
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Shannon Houck
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Xunkun Huang
- Department of Chemistry, Xiamen University, Xiamen 361005, China
| | - Kerwin Hui
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Bang C. Huynh
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Maxim Ivanov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Ádám Jász
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | - Hyunjun Ji
- Graduate School of Energy, Environment, Water and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Hanjie Jiang
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Benjamin Kaduk
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Sven Kähler
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Kirill Khistyaev
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Jaehoon Kim
- Graduate School of Energy, Environment, Water and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Gergely Kis
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | | | - Zsuzsanna Koczor-Benda
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Joong Hoon Koh
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Dimitri Kosenkov
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Laura Koulias
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | | | - Caroline M. Krauter
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Karl Kue
- Institute of Chemistry, Academia Sinica, 128, Academia Road Section 2, Nangang District, Taipei 11529, Taiwan
| | - Alexander Kunitsa
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Thomas Kus
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Arie Landau
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Keith V. Lawler
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Daniel Lefrancois
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | | | - Run R. Li
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Yi-Pei Li
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Jiashu Liang
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Marcus Liebenthal
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Hung-Hsuan Lin
- Institute of Chemistry, Academia Sinica, 128, Academia Road Section 2, Nangang District, Taipei 11529, Taiwan
| | - You-Sheng Lin
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Fenglai Liu
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | | | | | - Arne Luenser
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Aaditya Manjanath
- Institute of Chemistry, Academia Sinica, 128, Academia Road Section 2, Nangang District, Taipei 11529, Taiwan
| | - Prashant Manohar
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Erum Mansoor
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Sam F. Manzer
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Shan-Ping Mao
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | | | - Thomas Markovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Stephen Mason
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Simon A. Maurer
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Peter F. McLaughlin
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | | | - Jan-Michael Mewes
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Stefanie A. Mewes
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Pierpaolo Morgante
- Department of Chemistry, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | - J. Wayne Mullinax
- Department of Chemistry, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | | | | | - Alexander C. Paul
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Suranjan K. Paul
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Fabijan Pavošević
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Zheng Pei
- School of Electrical and Computer Engineering, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Stefan Prager
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Emil I. Proynov
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Ádám Rák
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | - Eloy Ramos-Cordoba
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Bhaskar Rana
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Alan E. Rask
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Adam Rettig
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Ryan M. Richard
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Fazle Rob
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Elliot Rossomme
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Tarek Scheele
- Institute for Physical and Theoretical Chemistry, University of Bremen, Bremen, Germany
| | - Maximilian Scheurer
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Matthias Schneider
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Nickolai Sergueev
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Shaama M. Sharada
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Wojciech Skomorowski
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - David W. Small
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Christopher J. Stein
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Yu-Chuan Su
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Eric J. Sundstrom
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Zhen Tao
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Jonathan Thirman
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Gábor J. Tornai
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | - Takashi Tsuchimochi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Norm M. Tubman
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Oleg Vydrov
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jan Wenzel
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Jon Witte
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Atsushi Yamada
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Kun Yao
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Sina Yeganeh
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Shane R. Yost
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Alexander Zech
- Department of Physical Chemistry, University of Geneva, 30, Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Igor Ying Zhang
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Xing Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Yu Zhang
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Dmitry Zuev
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Alán Aspuru-Guzik
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Alexis T. Bell
- Department of Chemical Engineering, University of California, Berkeley, California 94720, USA
| | - Nicholas A. Besley
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Ksenia B. Bravaya
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Bernard R. Brooks
- Laboratory of Computational Biophysics, National Institute of Health, Bethesda, Maryland 20892, USA
| | - David Casanova
- Donostia International Physics Center, 20080 Donostia, Euskadi, Spain
| | | | - Sonia Coriani
- Department of Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kgs Lyngby, Denmark
| | | | | | - A. Eugene DePrince
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Robert A. DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Barry D. Dunietz
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Thomas R. Furlani
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
| | - William A. Goddard
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, USA
| | | | - Teresa Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | | | | | - Yousung Jung
- Graduate School of Energy, Environment, Water and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Andreas Klamt
- COSMOlogic GmbH & Co. KG, Imbacher Weg 46, D-51379 Leverkusen, Germany
| | - Jing Kong
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Daniel S. Lambrecht
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | | | | | - C. William McCurdy
- Department of Chemistry, University of California, Davis, California 95616, USA
| | - Jeffrey B. Neaton
- Department of Physics, University of California, Berkeley, California 94720, USA
| | - Christian Ochsenfeld
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - John A. Parkhill
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Roberto Peverati
- Department of Chemistry, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | - Vitaly A. Rassolov
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
| | | | | | | | - Ryan P. Steele
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Joseph E. Subotnik
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Alex J. W. Thom
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Donald G. Truhlar
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Troy Van Voorhis
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Tomasz A. Wesolowski
- Department of Physical Chemistry, University of Geneva, 30, Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - K. Birgitta Whaley
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - H. Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, USA
| | - Paul M. Zimmerman
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Shirin Faraji
- Zernike Institute for Advanced Materials, University of Groningen, 9774AG Groningen, The Netherlands
| | | | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA,Author to whom correspondence should be addressed:
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35
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Quantum chemical calculations of lithium-ion battery electrolyte and interphase species. Sci Data 2021; 8:203. [PMID: 34354089 PMCID: PMC8342431 DOI: 10.1038/s41597-021-00986-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/22/2021] [Indexed: 02/07/2023] Open
Abstract
Lithium-ion batteries (LIBs) represent the state of the art in high-density energy storage. To further advance LIB technology, a fundamental understanding of the underlying chemical processes is required. In particular, the decomposition of electrolyte species and associated formation of the solid electrolyte interphase (SEI) is critical for LIB performance. However, SEI formation is poorly understood, in part due to insufficient exploration of the vast reactive space. The Lithium-Ion Battery Electrolyte (LIBE) dataset reported here aims to provide accurate first-principles data to improve the understanding of SEI species and associated reactions. The dataset was generated by fragmenting a set of principal molecules, including solvents, salts, and SEI products, and then selectively recombining a subset of the fragments. All candidate molecules were analyzed at the ωB97X-V/def2-TZVPPD/SMD level of theory at various charges and spin multiplicities. In total, LIBE contains structural, thermodynamic, and vibrational information on over 17,000 unique species. In addition to studies of reactivity in LIBs, this dataset may prove useful for machine learning of molecular and reaction properties.
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36
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Paul SK, Herbert JM. Probing Interfacial Effects on Ionization Energies: The Surprising Banality of Anion-Water Hydrogen Bonding at the Air/Water Interface. J Am Chem Soc 2021; 143:10189-10202. [PMID: 34184532 DOI: 10.1021/jacs.1c03131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Liquid microjet photoelectron spectroscopy is an increasingly common technique to measure vertical ionization energies (VIEs) of aqueous solutes, but the interpretation of these experiments is subject to questions regarding sensitivity to bulk versus interfacial solvation environments. We have computed aqueous-phase VIEs for a set of inorganic anions, using a combination of molecular dynamics simulations and electronic structure calculations, with results that are in excellent agreement with experiment regardless of whether the simulation data are restricted to ions at the air/water interface or to those in bulk aqueous solution. Although the computed VIEs are sensitive to ion-water hydrogen bonding, we find that the short-range solvation structure is sufficiently similar in both environments that it proves impossible to discriminate between the two on the basis of the VIE, a conclusion that has important implications for the interpretation of liquid-phase photoelectron spectroscopy. More generally, analysis of the simulation data suggests that the surface activity of soft anions is largely a second or third solvation shell effect, arising from disruption of water-water hydrogen bonds and not from significant changes in first-shell anion-water hydrogen bonding.
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Affiliation(s)
- Suranjan K Paul
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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37
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Eriksen JJ. Decomposed Mean-Field Simulations of Local Properties in Condensed Phases. J Phys Chem Lett 2021; 12:6048-6055. [PMID: 34165982 DOI: 10.1021/acs.jpclett.1c01375] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The present work demonstrates a robust protocol for probing localized electronic structure in condensed-phase systems, operating in terms of a recently proposed theory for decomposing the results of Kohn-Sham density functional theory in a basis of spatially localized molecular orbitals. In an initial application to liquid, ambient water and the assessment of the solvation energy and the embedded dipole moment of H2O in solution, we find that both properties are amplified on average-in accordance with expectation-and that correlations are indeed observed to exist between them. However, the simulated solvent-induced shift to the dipole moment of water is found to be significantly dampened with respect to typical literature values. The local nature of our methodology has further allowed us to evaluate the convergence of bulk properties with respect to the extent of the underlying one-electron basis set, ranging from single-ζ to full (augmented) quadruple-ζ quality. Albeit a pilot example, our work paves the way toward future studies of local effects and defects in more complex phases, e.g., liquid mixtures and even solid-state crystals.
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Affiliation(s)
- Janus J Eriksen
- DTU Chemistry, Technical University of Denmark, Kemitorvet Bldg. 206, DK-2800 Kgs. Lyngby, Denmark
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38
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Price AJA, Bryenton KR, Johnson ER. Requirements for an accurate dispersion-corrected density functional. J Chem Phys 2021; 154:230902. [PMID: 34241263 DOI: 10.1063/5.0050993] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Post-self-consistent dispersion corrections are now the norm when applying density-functional theory to systems where non-covalent interactions play an important role. However, there is a wide range of base functionals and dispersion corrections available from which to choose. In this work, we opine on the most desirable requirements to ensure that both the base functional and dispersion correction, individually, are as accurate as possible for non-bonded repulsion and dispersion attraction. The base functional should be dispersionless, numerically stable, and involve minimal delocalization error. Simultaneously, the dispersion correction should include finite damping, higher-order pairwise dispersion terms, and electronic many-body effects. These criteria are essential for avoiding reliance on error cancellation and obtaining correct results from correct physics.
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Affiliation(s)
- Alastair J A Price
- Department of Chemistry, Dalhousie University, 6274 Coburg Rd., Halifax, Nova Scotia B3H 4R2, Canada
| | - Kyle R Bryenton
- Department of Physics and Atmospheric Science, Dalhousie University, 6310 Coburg Rd., Halifax, Nova Scotia B3H 4R2, Canada
| | - Erin R Johnson
- Department of Chemistry, Dalhousie University, 6274 Coburg Rd., Halifax, Nova Scotia B3H 4R2, Canada
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39
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Mitra S, Werling K, Berquist EJ, Lambrecht DS, Garrett-Roe S. CH Mode Mixing Determines the Band Shape of the Carboxylate Symmetric Stretch in Apo-EDTA, Ca 2+-EDTA, and Mg 2+-EDTA. J Phys Chem A 2021; 125:4867-4881. [PMID: 34042451 DOI: 10.1021/acs.jpca.1c03061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The infrared spectra of EDTA complexed with Ca2+ and Mg2+ contain, to date, unidentified vibrational bands. This study assigns the peaks in the linear and two-dimensional infrared spectra of EDTA, with and without either Ca2+ or Mg2+ ions. Two-dimensional infrared spectroscopy and DFT calculations reveal that, in both the presence and absence of ions, the carboxylate symmetric stretch and the terminal CH bending vibrations mix. We introduce a method to calculate participation coefficients that quantify the contribution of the carboxylate symmetric stretch, CH wag, CH twist, and CH scissor in the 1400-1550 cm-1 region. With the help of participation coefficients, we assign the 1400-1430 cm-1 region to the carboxylate symmetric stretch, which can mix with CH modes. We assign the 1000-1380 cm-1 region to CH twist modes, the 1380-1430 cm-1 region to wag modes, and the 1420-1650 cm-1 region to scissor modes. The difference in binding geometry between the carboxylate-Ca2+ and carboxylate-Mg2+ complex manifests as new diagonal and cross-peaks between the mixed modes in the two complexes. The small Mg2+ ion binds EDTA tighter than the Ca2+ ion, which causes a redshift of the COO symmetric stretches of the sagittal carboxylates. Energy decomposition analysis further characterizes the importance of electrostatics and deformation energy in the bound complexes.
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Affiliation(s)
- Sunayana Mitra
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Keith Werling
- School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Eric J Berquist
- Q-Chem Incorporated, 6601 Owens Drive, Suite 105, Pleasanton, California 94588, United States
| | - Daniel S Lambrecht
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States.,Department of Chemistry and Physics, Florida Gulf Coast University, Fort Myers, Florida 33965, United States
| | - Sean Garrett-Roe
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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40
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Santra G, Cho M, Martin JML. Exploring Avenues beyond Revised DSD Functionals: I. Range Separation, with xDSD as a Special Case. J Phys Chem A 2021; 125:4614-4627. [PMID: 34009986 PMCID: PMC8279641 DOI: 10.1021/acs.jpca.1c01294] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/06/2021] [Indexed: 01/16/2023]
Abstract
We have explored the use of range separation as a possible avenue for further improvement on our revDSD minimally empirical double hybrid functionals. Such ωDSD functionals encompass the XYG3 type of double hybrid (i.e., xDSD) as a special case for ω → 0. As in our previous studies, the large and chemically diverse GMTKN55 benchmark suite was used for evaluation. Especially when using the D4 rather than D3BJ dispersion model, xDSD has a slight performance advantage in WTMAD2. As in previous studies, PBEP86 is the winning combination for the semilocal parts. xDSDn-PBEP86-D4 marginally outperforms the previous "best in class" ωB97M(2) Berkeley double hybrid but without range separation and using fewer than half the number of empirical parameters. Range separation turns out to offer only marginal further improvements on GMTKN55 itself. While ωB97M(2) still yields better performance for small-molecule thermochemistry, this is compensated in WTMAD2 by the superior performance of the new functionals for conformer equilibria. Results for two external test sets with pronounced static correlation effects may indicate that range-separated double hybrids are more resilient to such effects.
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Affiliation(s)
- Golokesh Santra
- Department
of Organic Chemistry, Weizmann Institute
of Science, 7610001 Reḥovot, Israel
| | - Minsik Cho
- Department
of Organic Chemistry, Weizmann Institute
of Science, 7610001 Reḥovot, Israel
- Department
of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Jan M. L. Martin
- Department
of Organic Chemistry, Weizmann Institute
of Science, 7610001 Reḥovot, Israel
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41
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Shee J, Loipersberger M, Hait D, Lee J, Head-Gordon M. Revealing the nature of electron correlation in transition metal complexes with symmetry breaking and chemical intuition. J Chem Phys 2021; 154:194109. [PMID: 34240907 DOI: 10.1063/5.0047386] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, we provide a nuanced view of electron correlation in the context of transition metal complexes, reconciling computational characterization via spin and spatial symmetry breaking in single-reference methods with qualitative concepts from ligand-field and molecular orbital theories. These insights provide the tools to reliably diagnose the multi-reference character, and our analysis reveals that while strong (i.e., static) correlation can be found in linear molecules (e.g., diatomics) and weakly bound and antiferromagnetically coupled (monometal-noninnocent ligand or multi-metal) complexes, it is rarely found in the ground-states of mono-transition-metal complexes. This leads to a picture of static correlation that is no more complex for transition metals than it is, e.g., for organic biradicaloids. In contrast, the ability of organometallic species to form more complex interactions, involving both ligand-to-metal σ-donation and metal-to-ligand π-backdonation, places a larger burden on a theory's treatment of dynamic correlation. We hypothesize that chemical bonds in which inter-electron pair correlation is non-negligible cannot be adequately described by theories using MP2 correlation energies and indeed find large errors vs experiment for carbonyl-dissociation energies from double-hybrid density functionals. A theory's description of dynamic correlation (and to a less important extent, delocalization error), which affects relative spin-state energetics and thus spin symmetry breaking, is found to govern the efficacy of its use to diagnose static correlation.
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Affiliation(s)
- James Shee
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Matthias Loipersberger
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Diptarka Hait
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Joonho Lee
- Department of Chemistry, Columbia University, New York, New York 10027, USA
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
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42
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Matz F, Music A, Didier D, Jagau T. Computational insights into electrochemical cross‐coupling of quaternary borate salts. ELECTROCHEMICAL SCIENCE ADVANCES 2021. [DOI: 10.1002/elsa.202100032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Florian Matz
- Division of Quantum Chemistry and Physical Chemistry KU Leuven Leuven Belgium
- Institute for Physical and Electrochemistry Leibniz University Hanover Hanover Germany
| | - Arif Music
- Department of Chemistry Ludwig Maximilian University of Munich Munich Germany
| | - Dorian Didier
- Department of Chemistry Ludwig Maximilian University of Munich Munich Germany
| | - Thomas‐C. Jagau
- Division of Quantum Chemistry and Physical Chemistry KU Leuven Leuven Belgium
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43
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Herbert JM. Dielectric continuum methods for quantum chemistry. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1519] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- John M. Herbert
- Department of Chemistry and Biochemistry The Ohio State University Columbus Ohio USA
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44
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Santra G, Martin JML. What Types of Chemical Problems Benefit from Density-Corrected DFT? A Probe Using an Extensive and Chemically Diverse Test Suite. J Chem Theory Comput 2021; 17:1368-1379. [PMID: 33625863 PMCID: PMC8028055 DOI: 10.1021/acs.jctc.0c01055] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
![]()
For the large and
chemically diverse GMTKN55 benchmark suite, we
have studied the performance of density-corrected density functional
theory (HF-DFT), compared to self-consistent DFT, for several pure
and hybrid GGA and meta-GGA exchange–correlation (XC) functionals
(PBE, BLYP, TPSS, and SCAN) as a function of the percentage of HF
exchange in the hybrid. The D4 empirical dispersion correction has
been added throughout. For subsets dominated by dynamical correlation,
HF-DFT is highly beneficial, particularly at low HF exchange percentages.
This is especially true for noncovalent interactions where the electrostatic
component is dominant, such as hydrogen and halogen bonds: for π-stacking,
HF-DFT is detrimental. For subsets with significant nondynamical correlation
(i.e., where a Hartree–Fock determinant is not a good zero-order
wavefunction), HF-DFT may do more harm than good. While the self-consistent
series show optima at or near 37.5% (i.e., 3/8) for all four XC functionals—consistent
with Grimme’s proposal of the PBE38 functional—HF-BnLYP-D4, HF-PBEn-D4, and HF-TPSSn-D4 all exhibit minima nearer 25% (i.e., 1/4) as the use
of HF orbitals greatly mitigates the error at 25% for barrier heights.
Intriguingly, for HF-SCANn-D4, the minimum is near
10%, but the weighted mean absolute error (WTMAD2) for GMTKN55 is
only barely lower than that for HF-SCAN-D4 (i.e., where the post-HF
step is a pure meta-GGA). The latter becomes an attractive option,
only slightly more costly than pure Hartree–Fock, and devoid
of adjustable parameters other than the three in the dispersion correction.
Moreover, its WTMAD2 is only surpassed by the highly empirical M06-2X
and by the combinatorially optimized empirical range-separated hybrids
ωB97X-V and ωB97M-V.
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Affiliation(s)
- Golokesh Santra
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Reḥovot, Israel
| | - Jan M L Martin
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Reḥovot, Israel
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45
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Herbert JM, Carter-Fenk K. Electrostatics, Charge Transfer, and the Nature of the Halide-Water Hydrogen Bond. J Phys Chem A 2021; 125:1243-1256. [PMID: 33502859 DOI: 10.1021/acs.jpca.0c11356] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Binary halide-water complexes X-(H2O) are examined by means of symmetry-adapted perturbation theory, using charge-constrained promolecular reference densities to extract a meaningful charge-transfer component from the induction energy. As is known, the X-(H2O) potential energy surface (for X = F, Cl, Br, or I) is characterized by symmetric left and right hydrogen bonds separated by a C2v-symmetric saddle point, with a tunneling barrier height that is <2 kcal/mol except in the case of F-(H2O). Our analysis demonstrates that the charge-transfer energy is correspondingly small (<2 kcal/mol except for X = F), considerably smaller than the electrostatic interaction energy. Nevertheless, charge transfer plays a crucial role determining the conformational preferences of X-(H2O) and provides a driving force for the formation of quasi-linear X··· H-O hydrogen bonds. Charge-transfer energies correlate well with measured O-H vibrational redshifts for the halide-water complexes and also for OH-(H2O) and NO2-(H2O), providing some indication of a general mechanism.
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Affiliation(s)
- John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Kevin Carter-Fenk
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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46
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PyVibMS: a PyMOL plugin for visualizing vibrations in molecules and solids. J Mol Model 2020; 26:290. [PMID: 32986131 DOI: 10.1007/s00894-020-04508-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/04/2020] [Indexed: 02/05/2023]
Abstract
Visualizing vibrational motions calculated with different ab initio packages requires dedicated post-processing tools. Here, we present a PyMOL plugin called PyVibMS for visualizing the vibrational motions for both molecular and solid systems calculated by mainstream quantum chemical computer programs including Gaussian, Q-Chem, VASP, and CRYSTAL. Benefiting from the continuing development of the PyMOL platform, PyVibMS provides powerful functionalities and user-friendly interface. PyVibMS was written in Python and its open-source nature makes it flexible and sustainable. As an example, the motions of the Konkoli-Cremer local vibrational modes are shown in this work for the first time. PyVibMS is freely available at https://github.com/smutao/PyVibMS . Graphical abstract In this work, a PyMOL plugin named PyVibMS is developed to visualize molecular and lattice vibrations.
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47
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Yamamoto Y, Salcedo A, Diaz CM, Alam MS, Baruah T, Zope RR. Assessing the effect of regularization on the molecular properties predicted by SCAN and self-interaction corrected SCAN meta-GGA. Phys Chem Chem Phys 2020; 22:18060-18070. [PMID: 32760934 DOI: 10.1039/d0cp02717k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recent regularization of the SCAN meta-GGA functional (rSCAN) has simplified the numerical complexities of the SCAN functional, alleviating SCAN's stringent demand on the numerical integration grids to some extent. The regularization of rSCAN, however, results in the breaking of some constraints such as the uniform electron gas limit, the slowly varying density limit, and coordinate scaling of the iso-orbital indicator. Here, we assess the effects of regularization on the electronic, structural, vibrational, and magnetic properties of molecules by comparing the SCAN and rSCAN predictions. The properties studied include atomic energies, atomization energies, ionization potentials, electron affinities, barrier heights, infrared intensities, dissociation and reaction energies, spin moments of molecular magnets, and isomer ordering of water clusters. Our results show that rSCAN requires less dense numerical grids and gives very similar results to those of SCAN for all properties examined with the exception of atomization energies, which are worsened in rSCAN. We also examine the performance of self-interaction-corrected (SIC) rSCAN with respect to SIC-SCAN using the Perdew-Zunger (PZ) SIC method. The PZSIC method uses orbital densities to compute one-electron self-interaction errors and places an even more stringent demand on numerical grids. Our results show that SIC-rSCAN gives marginally better performance than SIC-SCAN for almost all properties studied in this work with numerical grids that are on average half or less as dense as that needed for SIC-SCAN.
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Affiliation(s)
- Yoh Yamamoto
- Department of Physics, The University of Texas at El Paso, El Paso, Texas 79968, USA.
| | - Alan Salcedo
- Department of Physics, The University of Texas at El Paso, El Paso, Texas 79968, USA.
| | - Carlos M Diaz
- Department of Physics, The University of Texas at El Paso, El Paso, Texas 79968, USA. and Computational Science Program, The University of Texas at El Paso, El Paso, Texas 79968, USA
| | - Md Shamsul Alam
- Department of Physics, The University of Texas at El Paso, El Paso, Texas 79968, USA. and Computational Science Program, The University of Texas at El Paso, El Paso, Texas 79968, USA
| | - Tunna Baruah
- Department of Physics, The University of Texas at El Paso, El Paso, Texas 79968, USA. and Computational Science Program, The University of Texas at El Paso, El Paso, Texas 79968, USA
| | - Rajendra R Zope
- Department of Physics, The University of Texas at El Paso, El Paso, Texas 79968, USA. and Computational Science Program, The University of Texas at El Paso, El Paso, Texas 79968, USA
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48
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Paquier J, Giner E, Toulouse J. Relativistic short-range exchange energy functionals beyond the local-density approximation. J Chem Phys 2020; 152:214106. [DOI: 10.1063/5.0004926] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Julien Paquier
- Laboratoire de Chimie Théorique (LCT), Sorbonne Université and CNRS, F-75005 Paris, France
| | - Emmanuel Giner
- Laboratoire de Chimie Théorique (LCT), Sorbonne Université and CNRS, F-75005 Paris, France
| | - Julien Toulouse
- Laboratoire de Chimie Théorique (LCT), Sorbonne Université and CNRS, F-75005 Paris, France
- Institut Universitaire de France, F-75005 Paris, France
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49
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Grambow CA, Pattanaik L, Green WH. Reactants, products, and transition states of elementary chemical reactions based on quantum chemistry. Sci Data 2020; 7:137. [PMID: 32385318 PMCID: PMC7210263 DOI: 10.1038/s41597-020-0460-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/24/2020] [Indexed: 01/12/2023] Open
Abstract
Reaction times, activation energies, branching ratios, yields, and many other quantitative attributes are important for precise organic syntheses and generating detailed reaction mechanisms. Often, it would be useful to be able to classify proposed reactions as fast or slow. However, quantitative chemical reaction data, especially for atom-mapped reactions, are difficult to find in existing databases. Therefore, we used automated potential energy surface exploration to generate 12,000 organic reactions involving H, C, N, and O atoms calculated at the ωB97X-D3/def2-TZVP quantum chemistry level. We report the results of geometry optimizations and frequency calculations for reactants, products, and transition states of all reactions. Additionally, we extracted atom-mapped reaction SMILES, activation energies, and enthalpies of reaction. We believe that this data will accelerate progress in automated methods for organic synthesis and reaction mechanism generation—for example, by enabling the development of novel machine learning models for quantitative reaction prediction. Measurement(s) | activation energy • Standard Transformed Enthalpy Change • transition state • reactant • reaction product • chemical reaction • SMILES string | Technology Type(s) | quantum chemistry computational method |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.12047193
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Affiliation(s)
- Colin A Grambow
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139, United States
| | - Lagnajit Pattanaik
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139, United States
| | - William H Green
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139, United States.
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50
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Fabrizio A, Petraglia R, Corminboeuf C. Balancing Density Functional Theory Interaction Energies in Charged Dimers Precursors to Organic Semiconductors. J Chem Theory Comput 2020; 16:3530-3542. [DOI: 10.1021/acs.jctc.9b01193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Alberto Fabrizio
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Riccardo Petraglia
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Clemence Corminboeuf
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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