1
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Schreder L, Luber S. Implementation of frozen density embedding in CP2K and OpenMolcas: CASSCF wavefunctions embedded in a Gaussian and plane wave DFT environment. J Chem Phys 2024; 161:144110. [PMID: 39387407 DOI: 10.1063/5.0222409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 09/18/2024] [Indexed: 10/15/2024] Open
Abstract
Most chemical processes happen at a local scale where only a subset of molecular orbitals is directly involved and only a subset of covalent bonds may be rearranged. To model such reactions, Density Functional Theory (DFT) is often inadequate, and the use of computationally more expensive correlated wavefunction (WF) methods is required for accurate results. Mixed-resolution approaches backed by quantum embedding theory have been used extensively to approach this imbalance. Based on the frozen density embedding freeze-and-thaw algorithm, we describe an approach to embed complete active space self-consistent field simulations run in the OpenMolcas code in a DFT environment calculated in CP2K without requiring any external tools. This makes it possible to study a local, active part of a chemical system in a larger and relatively static environment with a computational cost balanced between the accuracy of a WF method and the efficiency of DFT, which we test on environment-subsystem pairs. Finally, we apply the implementation to an oxygen molecule leaving an aluminum (111) surface and a ruthenium(IV) oxide (110) surface.
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Affiliation(s)
- Lukas Schreder
- University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Sandra Luber
- University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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2
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Cafiero M. Role of Exact Exchange and Empirical Dispersion in Density Functional Theory-Based Three-Body Noncovalent Interactions. J Phys Chem A 2024; 128:8777-8786. [PMID: 39320094 DOI: 10.1021/acs.jpca.4c03262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2024]
Abstract
Total and three-body interaction energies are calculated for a benchmark set of three-body systems using a range of different types of density functional theory (DFT) methods, with the results compared to CCSD(T)/CBS results from the benchmark reference [Phys. Chem. Chem. Phys. 2023, 25, 28621-28637]. Inclusion of Hartree-Fock exchange, via either a global or range-separated hybrid approach or inclusion of empirical dispersion corrections, increases accuracy for total and three-body interactions. Basis set convergence testing shows that the aug-cc-pVTZ basis set is well converged with little to no change seen when using quadruple-ζ basis sets. The accuracy of the DFT methods is similar when calculating interaction energies for both global and local minimum structures. Overall, the CAM-B3LYP-D3BJ, B97D3, and ωB97XD functionals are recommended for calculating three-body interactions.
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Affiliation(s)
- Mauricio Cafiero
- Department of Chemistry, University of Reading, Whiteknights Campus, Reading RG6 6UR, U.K
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3
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Perrella F, Petrone A, Rega N. Second-Order Mass-Weighting Scheme for Atom-Centered Density Matrix Propagation Molecular Dynamics. J Chem Theory Comput 2024. [PMID: 39382519 DOI: 10.1021/acs.jctc.4c01031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2024]
Abstract
The atom-centered density matrix propagation (ADMP) method is an extended Lagrangian approach to ab initio molecular dynamics, which includes the density matrix in an orthonormalized atom-centered Gaussian basis as additional, fictitious, electronic degrees of freedom, classically propagated along with the nuclear ones. A high adiabaticity between the nuclear and electronic subsystems is mandatory in order to keep the trajectory close to the Born-Oppenheimer (BO) surface. In this regard, the fictitious electronic mass μ, being a symmetric, nondiagonal matrix in its most general form, represents a free parameter, exploitable to optimize the propagation of the electronic density. Although mass-weighting schemes in ADMP exist, a systematic procedure to define an optimal value of the fictitious masses is not available yet. In this work, in order to rationally evaluate the electronic mass, fictitious electronic normal modes are defined through the diagonalization of the Hessian of the electronic density matrix. If the same frequency is imposed on all such modes (compatible with the chosen integration time step), then the corresponding μ matrix can be calculated and then employed for the following propagation. Analysis of several ADMP test simulations reveals that such Hessian-based mass-weighting approach is able to ensure, together with a 0.1/0.2 fs time steps, a high separation between the (real) nuclear and the (fictitious) electronic frequencies, which determines a high adiabaticity. This high, unprecedented, accuracy in the propagation leads, in turn, to low errors in the estimated nuclear vibrational frequencies, making the ADMP method totally comparable to a fully converged BO molecular dynamics simulation but more computationally efficient. This work, therefore, contributes to a further development of the ADMP ab initio molecular dynamics method, aimed at improving its accuracy through a more rational evaluation of the fictitious electronic mass parameter.
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Affiliation(s)
- Fulvio Perrella
- Scuola Superiore Meridionale, Largo San Marcellino 10, Napoli I-80138, Italy
| | - Alessio Petrone
- Scuola Superiore Meridionale, Largo San Marcellino 10, Napoli I-80138, Italy
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di Monte S. Angelo, Via Cintia 21, Napoli I-80126, Italy
- Istituto Nazionale Di Fisica Nucleare, Sezione di Napoli, Complesso Universitario di Monte S. Angelo ed. 6, Via Cintia 21, Napoli I-80126, Italy
| | - Nadia Rega
- Scuola Superiore Meridionale, Largo San Marcellino 10, Napoli I-80138, Italy
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di Monte S. Angelo, Via Cintia 21, Napoli I-80126, Italy
- Istituto Nazionale Di Fisica Nucleare, Sezione di Napoli, Complesso Universitario di Monte S. Angelo ed. 6, Via Cintia 21, Napoli I-80126, Italy
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4
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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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5
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Shu Y, Zhu Z, Kanchanakungwankul S, Truhlar DG. Small Representative Databases for Testing and Validating Density Functionals and Other Electronic Structure Methods. J Phys Chem A 2024. [PMID: 39046238 DOI: 10.1021/acs.jpca.4c03137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Broad and diverse sets of accurate data provide useful metrics for assessing the performance of new theoretical methods. However, assessing methods against large databases can be an arduous task. Here, we present 17 representative energetic databases, defined as small databases whose errors and error spreads are representative of larger databases and which therefore can serve as efficient benchmarks for developing and testing electronic structure methods and density functionals. In 15 cases, the representative databases have 6 entries while being representative of larger databases with 14-107 entries, and in the other two cases, they have 14 entries while being representative of larger databases with 418-455 entries. The mean unsigned error (MUE) of 100 electronic structure methods on a given representative database is typically within about 8% of the MUE on its parent database, and the root-mean-square error (RMSE) is typically within about 11% of the RMSE on the parent database. Thus, the representative databases are quite successful in indicating accuracy while maintaining good diversity. The databases include both main-group and transition-metal compounds and reactions, and they include bond energies, reaction energies, barrier heights, noncovalent interactions, ionization potentials, and absolute energies.
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Affiliation(s)
- Yinan Shu
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Zhaohan Zhu
- Department of Biostatistics, University of Florida, Gainesville, Florida 32611, United States
| | - Siriluk Kanchanakungwankul
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
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6
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Vlasenko MP, Pozharskii AF, Ozeryanskii VA, Kletskii ME, Lisovin AV, Demidov OP, Tkachuk AV. Proton Sponge Zwitterions with Positively and Negatively Charged Hydrogen Bonds: Extremely Polar Organic Compounds and Interplay of [NHN] + and [NHN] - Properties. J Org Chem 2024; 89:9210-9222. [PMID: 38875486 DOI: 10.1021/acs.joc.3c02964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2024]
Abstract
Six previously unknown zwitterions with positively and negatively charged [NHN] hydrogen bonds were synthesized by acylation of 4,5-bis(dimethylamino)-1-tosylamino-8-aminonaphthalene with subsequent alkaline treatment of the resulting 8-acylamino derivatives. Using NMR and XRD measurements in conjunction with quantum chemical DFT/PBE1PBE/6-311++G(d,p) calculations, it was shown that the negatively charged [NHN]- bond in such compounds commonly differs from the [NHN]+ bond by significantly lower linearity, higher asymmetry, and moderate to strong paramagnetic shift of the chelated NH proton signal. Among other remarkable findings, the most important are (1) unusually high polarity (μ = 21-26 D) of the obtained zwitterions, (2) sharp difference in structures of the solid 1,8-bis(tosylated) zwitterion (BTZ) grown from MeCN or DMF, and (3) registration for one of the stereoisomers of BTZ with the record short [NHN]- hydrogen bridge (N···N = 2.510 Å) almost reaching the theoretical limit (2.50 Å) for the [NHN]+ hydrogen bond.
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Affiliation(s)
- Marina P Vlasenko
- Department of Chemistry, Southern Federal University, Zorge Street 7, 344090 Rostov-on-Don, Russian Federation
| | - Alexander F Pozharskii
- Department of Chemistry, Southern Federal University, Zorge Street 7, 344090 Rostov-on-Don, Russian Federation
| | - Valery A Ozeryanskii
- Department of Chemistry, Southern Federal University, Zorge Street 7, 344090 Rostov-on-Don, Russian Federation
| | - Mikhail E Kletskii
- Department of Chemistry, Southern Federal University, Zorge Street 7, 344090 Rostov-on-Don, Russian Federation
| | - Anton V Lisovin
- Institute of Physical and Organic Chemistry, Southern Federal University, Stachki Avenue 194/2, 344090 Rostov-on-Don, Russian Federation
| | - Oleg P Demidov
- Department of Chemistry, North Caucasus Federal University, Pushkin Street 1, 355017 Stavropol, Russian Federation
| | - Anna V Tkachuk
- Department of Chemistry, Southern Federal University, Zorge Street 7, 344090 Rostov-on-Don, Russian Federation
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7
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Iuzzolino G, Perrella F, Valadan M, Petrone A, Altucci C, Rega N. Photophysics of a nucleic acid-protein crosslinking model strongly depends on solvation dynamics: an experimental and theoretical study. Phys Chem Chem Phys 2024; 26:11755-11769. [PMID: 38563904 DOI: 10.1039/d3cp06254f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
We present a combined experimental and theoretical study of the photophysics of 5-benzyluracil (5BU) in methanol, which is a model system for interactions between nucleic acids and proteins. A molecular dynamics study of 5BU in solution through efficient DFT-based hybrid ab initio potentials revealed a remarkable conformational flexibility - allowing the population of two main conformers - as well as specific solute-solvent interactions, which both appear as relevant factors for the observed 5BU optical absorption properties. The simulated absorption spectrum, calculated on such an ensemble, enabled a molecular interpretation of the experimental UV-Vis lowest energy band, which is also involved in the induced photo-reactivity upon irradiation. In particular, the first two excited states (mainly involving the uracil moiety) both contribute to the 5BU lowest energy absorption. Moreover, as a key finding, the nature and brightness of such electronic transitions are strongly influenced by 5BU conformation and the microsolvation of its heteroatoms.
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Affiliation(s)
- Gabriele Iuzzolino
- Scuola Superiore Meridionale, Largo San Marcellino 10, Napoli I-80138, Italy
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, via Cintia 21, Napoli I-80126, Italy.
| | - Fulvio Perrella
- Scuola Superiore Meridionale, Largo San Marcellino 10, Napoli I-80138, Italy
| | - Mohammadhassan Valadan
- Dipartimento di Scienze Biomediche Avanzate, Università degli Studi di Napoli Federico II, via Pansini 5, Napoli I-80131, Italy
- Istituto Nazionale di Fisica Nucleare, Unità di Napoli, via Cintia 21, Napoli I-80126, Italy
| | - Alessio Petrone
- Scuola Superiore Meridionale, Largo San Marcellino 10, Napoli I-80138, Italy
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, via Cintia 21, Napoli I-80126, Italy.
- Istituto Nazionale di Fisica Nucleare, Unità di Napoli, via Cintia 21, Napoli I-80126, Italy
| | - Carlo Altucci
- Dipartimento di Scienze Biomediche Avanzate, Università degli Studi di Napoli Federico II, via Pansini 5, Napoli I-80131, Italy
- Istituto Nazionale di Fisica Nucleare, Unità di Napoli, via Cintia 21, Napoli I-80126, Italy
- Istituto di Scienze Applicate e Sistemi Intelligenti "Eduardo Caianiello", URT UNINA, via Cintia 21, Napoli I-80126, Italy
| | - Nadia Rega
- Scuola Superiore Meridionale, Largo San Marcellino 10, Napoli I-80138, Italy
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, via Cintia 21, Napoli I-80126, Italy.
- Istituto Nazionale di Fisica Nucleare, Unità di Napoli, via Cintia 21, Napoli I-80126, Italy
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8
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Subramani M, Saravanan V, Muralidharan A, Durai R, Ramasamy S. Theoretical insights on the development of a 55-77 graphene sheet by embedding Ag n=1-4 and Pd n=1-4 metal nanoclusters for efficient CO 2 capture. J Mol Graph Model 2023; 124:108573. [PMID: 37523943 DOI: 10.1016/j.jmgm.2023.108573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/07/2023] [Accepted: 07/24/2023] [Indexed: 08/02/2023]
Abstract
Recent advancements in two-dimensional (2D) allotropes of carbon materials and their usage as superior CO2 adsorbents can decrease the detrimental impact of CO2 on climate change. With the use of quantum chemical calculations, the effect of metal clusters (Agn = 1-4 and Pdn = 1-4) on the structural and electrical characteristics of 55-77 2D graphene sheet is examined in the current work with an aim towards enhancing CO2 capture capacity. The findings revealed that the binding energy (Eb) of the 55-77 sheet decoration with Pdn = 1-4 metal clusters are greater owing to chemisorption by 1.17 eV, 1.69 eV, 0.27 eV, and 1.58 eV than the decoration with Agn = 1-4 clusters. Moreover, CO2 molecules adsorb on the Pdn = 1-4 cluster decorated systems having -0.35 eV, 0.83 eV, 1.53 eV, and -0.98 eV greater adsorption energies than on the Agn = 1-4 decorated 55-77 sheet due to a stronger charge transfer. Further, the findings of an atoms in molecules (AIM) study show that the interaction between CO2 and Pdn = 1-4 decorated 55-77 sheet is partially covalent and non-covalent, confirming the greater charge transfer between the CO2 molecule and Pdn = 1-4 decorated 55-77 systems. Moreover, the CO2 adsorption on Pdn = 1-4 decorated 55-77 systems is clearly demonstrated by non-covalent interaction (NCI) analysis to be a strong electrostatic interaction at sign(λ2)ρ = -0.05 a.u, and this is further supported by an electron localization function (ELF) map. The highest CO2 adsorption capacity is obtained for 55-77/Pd1+CO2 with the value of 6.27 wt % which concludes 55-77 sheet with Pdn decoration is a more suitable structure for CO2 adsorption than the Agn decorated system.
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Affiliation(s)
- Mohanapriya Subramani
- Molecular Simulation Laboratory, Department of Physics, Bharathiar University, Coimbatore, 641046, Tamil Nadu, India
| | - Vinnarasi Saravanan
- Chemical Engineering, Indian Institute of Technology Bombay, Maharashtra, India
| | - Akilesh Muralidharan
- Molecular Simulation Laboratory, Department of Physics, Bharathiar University, Coimbatore, 641046, Tamil Nadu, India
| | - Ravichandran Durai
- Molecular Simulation Laboratory, Department of Physics, Bharathiar University, Coimbatore, 641046, Tamil Nadu, India
| | - Shankar Ramasamy
- Molecular Simulation Laboratory, Department of Physics, Bharathiar University, Coimbatore, 641046, Tamil Nadu, India.
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9
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Jana S, Śmiga S, Constantin LA, Samal P. Semilocal Meta-GGA Exchange-Correlation Approximation from Adiabatic Connection Formalism: Extent and Limitations. J Phys Chem A 2023; 127:8685-8697. [PMID: 37811903 PMCID: PMC10591512 DOI: 10.1021/acs.jpca.3c03976] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/24/2023] [Indexed: 10/10/2023]
Abstract
The incorporation of a strong-interaction regime within the approximate semilocal exchange-correlation functionals still remains a very challenging task for density functional theory. One of the promising attempts in this direction is the recently proposed adiabatic connection semilocal correlation (ACSC) approach [Constantin, L. A.; Phys. Rev. B 2019, 99, 085117] allowing one to construct the correlation energy functionals by interpolation of the high and low-density limits for the given semilocal approximation. The current study extends the ACSC method to the meta-generalized gradient approximations (meta-GGA) level of theory, providing some new insights in this context. As an example, we construct the correlation energy functional on the basis of the high- and low-density limits of the Tao-Perdew-Staroverov-Scuseria (TPSS) functional. Arose in this way, the TPSS-ACSC functional is one-electron self-interaction free and accurate for the strictly correlated and quasi-two-dimensional regimes. Based on simple examples, we show the advantages and disadvantages of ACSC semilocal functionals and provide some new guidelines for future developments in this context.
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Affiliation(s)
- Subrata Jana
- Department
of Chemistry & Biochemistry, The Ohio
State University, Columbus, Ohio 43210, United States
| | - Szymon Śmiga
- Institute
of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Toruń, ul. Grudzikadzka 5, 87-100 Toruń, Poland
| | - Lucian A. Constantin
- Istituto
di Nanoscienze, Consiglio Nazionale delle
Ricerche CNR-NANO, 41125 Modena, Italy
| | - Prasanjit Samal
- School
of Physical Sciences, National Institute of Science Education and
Research, HBNI, Bhubaneswar 752050, India
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10
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Jana S, Constantin LA, Samal P. Density functional applications of jellium with a local gap model correlation energy functional. J Chem Phys 2023; 159:114109. [PMID: 37721324 DOI: 10.1063/5.0160961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/31/2023] [Indexed: 09/19/2023] Open
Abstract
We develop a realistic density functional approximation for the local gap, which is based on a semilocal indicator that shows good screening properties. The local band model has remarkable density scaling behaviors and works properly for the helium isoelectronic series for the atoms of the Periodic Table, as well as for the non-relativistic noble atom series (up to 2022 e-). Due to these desirable properties, we implement the local gap model in the jellium-with-gap correlation energy, developing the local-density-approximation-with-gap correlation functional (named LDAg) that correctly gives correlation energies of atoms comparable with the LDA ones but shows an improvement for ionization potential of atoms and molecules. Thus, LDAg seems to be an interesting and useful tool in density functional theory.
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Affiliation(s)
- Subrata Jana
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovoth 76100, Israel
| | - Lucian A Constantin
- Institute for Microelectronics and Microsystems (CNR-IMM), Via Monteroni, Campus Unisalento, 73100 Lecce, Italy
| | - Prasanjit Samal
- School of Physical Sciences, National Institute of Science Education and Research, HBNI, Bhubaneswar 752050, India
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11
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Mondal S. Charge-Shifted Weak Noncovalent Interactions in the Atmospherically Important OCS Microhydrates. J Phys Chem A 2023; 127:3293-3304. [PMID: 36943720 DOI: 10.1021/acs.jpca.2c07670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Stratospheric aerosol, mainly comprising microhydrated carbonyl sulfide (OCS), is among the primary drivers of climate change. In this study, we investigate the effect of microhydration on the structure, energetics, and vibrational properties of the neutral OCS molecule using ab initio calculation, molecular electrostatic potential (MESP), topological analyses of electron density, and natural bond orbital (NBO) analyses. The complexation energy increases with the cluster size, and the first solvation shell of OCS consists of four water molecules that interact with the OCS moiety preferentially through SOCS···OW, OOCS···OW, and COCS···OW type of weak noncovalent interaction instead of the typical OOCS···H-OW and SOCS···H-OW H-bonds. These noncovalent interactions originate due to the electron shift from the water oxygen lone pair to the antibonding orbital of C═S [BD*(C═S)], sometimes via BD*(C═O), which substantially perturbs the bending mode of surrounding water molecules. The present study thus unravels the underlying relationship between the OCS atmospheric hydrolysis and the charge-shifted noncovalent interactions.
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Affiliation(s)
- Saptarsi Mondal
- School of Chemical Sciences, Indian Association for the Cultivation of Sciences, Kolkata 700032, India
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12
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Markham GD, Rostami H, Larkin JD, Bock CW. Models for boronic acid receptors II: a computational structural, bonding, and thermochemical investigation of the RB(OH)2∙H2O∙NH3 and RB(−OCH2CH2O−)∙NH3∙H2O potential energy surfaces (R = H, methyl, phenyl, and ortho-methyl-phenyl). Struct Chem 2023. [DOI: 10.1007/s11224-023-02131-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
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13
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Energetic, conformational and vibrational features of the tripeptide (Gly)3. Data from MP2 and DFT calculations. COMPUT THEOR CHEM 2023. [DOI: 10.1016/j.comptc.2022.113989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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14
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Garg S, Goel N. Photodegradation of dye using Polythiophene/ZnO nanocomposite: A computational approach. J Mol Graph Model 2022; 117:108285. [PMID: 35964365 DOI: 10.1016/j.jmgm.2022.108285] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/27/2022] [Accepted: 07/27/2022] [Indexed: 01/14/2023]
Abstract
Incorporating nanostructured photocatalysts in polymers is a strategic way to obtain novel water purification systems. Here, we present density functional theory (DFT) study of Polythiophene/Zinc oxide (PTh/ZnO) nanocomposite with high photocatalytic performance and stability which exhibits superior degradation of alizarine dye under the visible light condition with interaction energy of -149.55 kcal/mol between conducting polymer (PTh) and metal oxide, with PTh sponsoring more number of electrons to the conduction band of ZnO. The electrical and optical properties of optimized geometries of PTh/ZnO nanocomposite were studied by frontier molecular orbital analysis, natural bond orbital (NBO) charge simulation, natural electronic configuration, and UV-vis absorption spectra. The modulation of the energy band gap (∽ 2.60 eV) and exciton binding energy (∽ 0.36 eV) causes visible light absorption and hence enhances the photodegradation activity of PTh/ZnO. NBO analysis evidences the electron accepting behavior of ZnO in the composites as it withdraws electron cloud density of about 0.14e from the polymer unit.
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Affiliation(s)
- Shivangi Garg
- Computational and Theoretical Chemistry Group, Department of Chemistry & Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, Chandigarh, India
| | - Neetu Goel
- Computational and Theoretical Chemistry Group, Department of Chemistry & Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, Chandigarh, India.
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15
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Domagała M, Jabłoński M, Dubis AT, Zabel M, Pfitzner A, Palusiak M. Testing of Exchange-Correlation Functionals of DFT for a Reliable Description of the Electron Density Distribution in Organic Molecules. Int J Mol Sci 2022; 23:ijms232314719. [PMID: 36499046 PMCID: PMC9740346 DOI: 10.3390/ijms232314719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/08/2022] [Accepted: 11/18/2022] [Indexed: 11/27/2022] Open
Abstract
Researchers carrying out calculations using the DFT method face the problem of the correct choice of the exchange-correlation functional to describe the quantities they are interested in. This article deals with benchmark calculations aimed at testing various exchange-correlation functionals in terms of a reliable description of the electron density distribution in molecules. For this purpose, 30 functionals representing all rungs of Jacob's Ladder are selected and then the values of some QTAIM-based parameters are compared with their reference equivalents obtained at the CCSD/aug-cc-pVTZ level of theory. The presented results show that the DFT method undoubtedly has the greatest problems with a reliable description of the electron density distribution in multiple strongly polar bonds, such as C=O, and bonds associated with large electron charge delocalization. The performance of the tested functionals turned out to be unsystematic. Nevertheless, in terms of a reliable general description of QTAIM-based parameters, the M11, SVWN, BHHLYP, M06-HF, and, to a slightly lesser extent, also BLYP, B3LYP, and X3LYP functionals turned out to be the worst. It is alarming to find the most popular B3LYP functional in this group. On the other hand, in the case of the electron density at the bond critical point, being the most important QTAIM-based parameter, the M06-HF functional is especially discouraged due to the very poor description of the C=O bond. On the contrary, the VSXC, M06-L, SOGGA11-X, M06-2X, MN12-SX, and, to a slightly lesser extent, also TPSS, TPSSh, and B1B95 perform well in this respect. Particularly noteworthy is the overwhelming performance of double hybrids in terms of reliable values of bond delocalization indices. The results show that there is no clear improvement in the reliability of describing the electron density distribution with climbing Jacob's Ladder, as top-ranked double hybrids are also, in some cases, able to produce poor values compared to CCSD.
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Affiliation(s)
- Małgorzata Domagała
- Faculty of Chemistry, University of Lodz, Pomorska 163/165, 90-236 Lodz, Poland
| | - Mirosław Jabłoński
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100 Toruń, Poland
- Correspondence: ; Tel.: +48-056-611-4695
| | - Alina T. Dubis
- Faculty of Chemistry, University of Białystok, Ciołkowskiego 1K, 15-245 Białystok, Poland
| | - Manfred Zabel
- Institute of Inorganic Chemistry, University of Regensburg, Universitätsstr. 31, 93040 Regensburg, Germany
| | - Arno Pfitzner
- Institute of Inorganic Chemistry, University of Regensburg, Universitätsstr. 31, 93040 Regensburg, Germany
| | - Marcin Palusiak
- Faculty of Chemistry, University of Lodz, Pomorska 163/165, 90-236 Lodz, Poland
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16
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Benassi E, Vaganova T, Malykhin E, Gatilov Y, Nurtay L, Fan H. Intermolecular interactions in the crystalline structure of some polyhalogenated Di- And triamino Pyridines: Spectroscopical perspectives. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 281:121632. [PMID: 35868054 DOI: 10.1016/j.saa.2022.121632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/01/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
Supramolecular synthon is identified as a unit and provides important structural and energetic information in the study of organic crystals. However, the direct estimation of the supramolecular interaction remains challenging. In the present work six polyhalogenated di- or triamino pyridines were synthesised, their crystalline structure was characterised, and corresponding supramolecular synthons were studied using a combination of quantum mechanical calculations and FT-IR and Raman spectroscopy. Some distinctive features were identified especially for three vibrational normal modes (RNMs) related to the pyridine ring (viz. RNM1, RNM3 and RNM7) in the vibrational spectra (FT-IR and Raman) of the solid samples, which are due to the supramolecular interactions, hydrogen bond (hb) in particular, according to the quantum mechanical calculations. The comparison between the IR and Raman spectra of experimental and simulated results indicates that the adjacent intermolecular hydrogen bonds between two same molecules extensively exist in the solid samples. Moreover, some quantitative correlation was established among the dimerisation energies for hb dimers (hb1 dimers for compounds 1 and 2), the ring structure defined by the distribution of the substituents and quantitative characteristics of the vibrational spectra, for instance, the splitting magnitudes for RNM3(2) in IR spectra and the peak gap between RNM1 and RNM2 in Raman spectra.
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Affiliation(s)
- Enrico Benassi
- Novosibirsk State University, Pirogova ul. 2, Novosibirsk, 630090, Russia.
| | - Tamara Vaganova
- Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentyev Prospekt 9, Novosibirsk, 630090, Russia
| | - Evgenij Malykhin
- Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentyev Prospekt 9, Novosibirsk, 630090, Russia
| | - Yurij Gatilov
- Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentyev Prospekt 9, Novosibirsk, 630090, Russia
| | - Lazzat Nurtay
- Department of Chemistry, School of Sciences and Humanities, Nazarbayev University, Qabanbay Batyr 53, Nursultan, 010000, Kazakhstan
| | - Haiyan Fan
- Department of Chemistry, School of Sciences and Humanities, Nazarbayev University, Qabanbay Batyr 53, Nursultan, 010000, Kazakhstan
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17
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Windom ZW, Datta M, Huda MM, Sabuj MA, Rai N. Understanding speciation and solvation of glyphosate from first principles simulations. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Tan S, Wang Y, Zhang IY, Xu X. Assessment of advanced xDH@B3LYP methods in describing various potential energy curves driven by π- π, CH/ π, and SH/ π non-bonded interactions. CHINESE J CHEM PHYS 2022. [DOI: 10.1063/1674-0068/cjcp2206098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Accurate description of potential energy curves driven by non-bonded interactions remains a great challenge for pure density functional approximations (DFAs). It is because the R−6 decay behavior of dispersion cannot be intrinsically captured by the (semi)-local ingredients and the exact-exchange used in the popular hybrid DFAs. Overemphasizing the accuracy on the equilibrium region for the functional construction would likely deteriorate the overall performance on the other regions of potential energy surfaces. In consequence, the empirical dispersion correction becomes the standard component in DFAs to treat the non-bonded interactions. In this Letter, we demonstrate that without the use of empirical dispersion correction, doubly hybrid approximations, in particular two recently proposed revXYG3 and XYG7 functionals, hold the promise to have a balanced description of non-bonded interactions on the whole potential energy curves for several prototypes of π- π, CH/ π, and SH/ π interactions. The error of revXYG3 and XYG7 for non-bonded interactions is around 0.1 kcal/mol, and their potential energy curves almost coincide with the accurate CCSD(T)/CBS curves.
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Affiliation(s)
- Shiqian Tan
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Key Laboratory of Computational Physical Sciences, Shanghai Key Laboratory of Bioactive Small Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Yizhen Wang
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Key Laboratory of Computational Physical Sciences, Shanghai Key Laboratory of Bioactive Small Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Igor Ying Zhang
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Key Laboratory of Computational Physical Sciences, Shanghai Key Laboratory of Bioactive Small Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Xin Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Key Laboratory of Computational Physical Sciences, Shanghai Key Laboratory of Bioactive Small Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China
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19
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Wang L, Wang Y, Wang CS, Hao Q. An Application of Dipole–Dipole Interaction Model in Stacking Dimers Including Protonated Arginine Residue. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2022. [DOI: 10.1134/s0036024422090205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Divya R, Maalmarugan J, Patel R, Meena M, Nikolova MP, Vimalan M, Tamilselvan S, SenthilKannan K. Synthesis, experimental and computational characterizations of 8,9-dimethoxybenzo[b]naphtho[2,3-d] thiophene (DBNT) crystals for electro-mechano utilities. INORG CHEM COMMUN 2022. [DOI: 10.1016/j.inoche.2022.109249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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21
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Puthenkalathil RC, Ensing B. Fast Proton Transport in FeFe Hydrogenase via a Flexible Channel and a Proton Hole Mechanism. J Phys Chem B 2022; 126:403-411. [PMID: 35007078 PMCID: PMC8785182 DOI: 10.1021/acs.jpcb.1c08124] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
Di-iron hydrogenases
are a class of enzymes that are capable of
reducing protons to form molecular hydrogen with high efficiency.
In addition to the catalytic site, these enzymes have evolved dedicated
pathways to transport protons and electrons to the reaction center.
Here, we present a detailed study of the most likely proton transfer
pathway in such an enzyme using QM/MM molecular dynamics simulations.
The protons are transported through a channel lined out from the protein
exterior to the di-iron active site, by a series of hydrogen-bonded,
weakly acidic or basic, amino acids and two incorporated water molecules.
The channel shows remarkable flexibility, which is an essential feature
to quickly reset the hydrogen-bond direction in the channel after
each proton passing. Proton transport takes place via a “hole”
mechanism, rather than an excess proton mechanism, the free energy
landscape of which is remarkably flat, with a highest transition state
barrier of only 5 kcal/mol. These results confirm our previous assumptions
that proton transport is not rate limiting in the H2 formation
activity and that cysteine C299 may be considered protonated at physiological
pH conditions. Detailed understanding of this proton transport may
aid in the ongoing attempts to design artificial biomimetic hydrogenases
for hydrogen fuel production.
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Affiliation(s)
- Rakesh C Puthenkalathil
- Van 't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Bernd Ensing
- Van 't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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22
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Sparrow ZM, Ernst BG, Joo PT, Lao KU, DiStasio RA. NENCI-2021. I. A large benchmark database of non-equilibrium non-covalent interactions emphasizing close intermolecular contacts. J Chem Phys 2021; 155:184303. [PMID: 34773949 DOI: 10.1063/5.0068862] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, we present NENCI-2021, a benchmark database of ∼8000 Non-Equilibirum Non-Covalent Interaction energies for a large and diverse selection of intermolecular complexes of biological and chemical relevance. To meet the growing demand for large and high-quality quantum mechanical data in the chemical sciences, NENCI-2021 starts with the 101 molecular dimers in the widely used S66 and S101 databases and extends the scope of these works by (i) including 40 cation-π and anion-π complexes, a fundamentally important class of non-covalent interactions that are found throughout nature and pose a substantial challenge to theory, and (ii) systematically sampling all 141 intermolecular potential energy surfaces (PESs) by simultaneously varying the intermolecular distance and intermolecular angle in each dimer. Designed with an emphasis on close contacts, the complexes in NENCI-2021 were generated by sampling seven intermolecular distances along each PES (ranging from 0.7× to 1.1× the equilibrium separation) and nine intermolecular angles per distance (five for each ion-π complex), yielding an extensive database of 7763 benchmark intermolecular interaction energies (Eint) obtained at the coupled-cluster with singles, doubles, and perturbative triples/complete basis set [CCSD(T)/CBS] level of theory. The Eint values in NENCI-2021 span a total of 225.3 kcal/mol, ranging from -38.5 to +186.8 kcal/mol, with a mean (median) Eint value of -1.06 kcal/mol (-2.39 kcal/mol). In addition, a wide range of intermolecular atom-pair distances are also present in NENCI-2021, where close intermolecular contacts involving atoms that are located within the so-called van der Waals envelope are prevalent-these interactions, in particular, pose an enormous challenge for molecular modeling and are observed in many important chemical and biological systems. A detailed symmetry-adapted perturbation theory (SAPT)-based energy decomposition analysis also confirms the diverse and comprehensive nature of the intermolecular binding motifs present in NENCI-2021, which now includes a significant number of primarily induction-bound dimers (e.g., cation-π complexes). NENCI-2021 thus spans all regions of the SAPT ternary diagram, thereby warranting a new four-category classification scheme that includes complexes primarily bound by electrostatics (3499), induction (700), dispersion (1372), or mixtures thereof (2192). A critical error analysis performed on a representative set of intermolecular complexes in NENCI-2021 demonstrates that the Eint values provided herein have an average error of ±0.1 kcal/mol, even for complexes with strongly repulsive Eint values, and maximum errors of ±0.2-0.3 kcal/mol (i.e., ∼±1.0 kJ/mol) for the most challenging cases. For these reasons, we expect that NENCI-2021 will play an important role in the testing, training, and development of next-generation classical and polarizable force fields, density functional theory approximations, wavefunction theory methods, and machine learning based intra- and inter-molecular potentials.
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Affiliation(s)
- Zachary M Sparrow
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Brian G Ernst
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Paul T Joo
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Ka Un Lao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Robert A DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
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23
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Pernal K, Hapka M. Range‐separated multiconfigurational density functional theory methods. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1566] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Michał Hapka
- Lodz University of Technology Institute of Physics Lodz Poland
- Faculty of Chemistry University of Warsaw Warsaw Poland
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24
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Heindel JP, Herman KM, Aprà E, Xantheas SS. Guest-Host Interactions in Clathrate Hydrates: Benchmark MP2 and CCSD(T)/CBS Binding Energies of CH 4, CO 2, and H 2S in (H 2O) 20 Cages. J Phys Chem Lett 2021; 12:7574-7582. [PMID: 34347487 DOI: 10.1021/acs.jpclett.1c01884] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We present benchmark binding energies of naturally occurring gas molecules CH4, CO2, and H2S in the small cage, namely, the pentagonal dodecahedron (512) (H2O)20, which is one of the constituent cages of the 3 major lattices (structures I, II, and H) of clathrate hydrates. These weak interactions require higher levels of electron correlation and converge slowly with an increasing basis set to the complete basis set (CBS) limit, necessitating the use of large basis sets up to the aug-cc-pV5Z and subsequent correction for basis set superposition error (BSSE). For the host hollow (H2O)20 cages, we have identified a most stable isomer with binding energy of -200.8 ± 2.1 kcal/mol at the CCSD(T)/CBS limit (-199.2 ± 0.5 kcal/mol at the MP2/CBS limit). Additionally, we report converged second order Møller-Plesset (MP2) CBS binding energies for the encapsulation of guests in the (H2O)20 cage of -4.3 ± 0.1 for CH4@(H2O)20, -6.6 ± 0.1 for CO2@(H2O)20, and -8.5 ± 0.1 kcal/mol for H2S@(H2O)20, respectively. For CH4@(H2O)20, exhibiting the weakest encapsulation affinity among the three, we report CCSD(T)/aug-cc-pVTZ binding energies and, based on them, a CCSD(T)/CBS estimate of -4.75 ± 0.1 kcal/mol. To the best of our knowledge, the CCSD(T)/aug-cc-pVTZ calculation for CH4@(H2O)20 is the largest one reported to date (168 valence electrons, 1978 basis functions, and the correlation of 84 doubly occupied and 1873 virtual orbitals) and required a scalable implementation of the (T) module on 6144 nodes (350 208 cores) of the "Cori" supercomputer at the National Energy Research Supercomputing Center (NERSC) for a total execution time of 195 min (for the (T) part). These efficient scalable implementations of highly correlated methods offer the capability to obtain long-lasting benchmarks of intermolecular interactions in complex systems. They also provide a path toward parametrizing classical potentials needed to study the dynamical and transport properties in these complex systems as well as assess the accuracy of lower scaling electronic structure methods such as density functional theory (DFT) and MP2 including its spin-biased variants.
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Affiliation(s)
- Joseph P Heindel
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Kristina M Herman
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Edoardo Aprà
- William R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Sotiris S Xantheas
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
- Advanced Computing, Mathematics and Data Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, Washington 99352, United States
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25
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Sen R, González-Espinoza CE, Zech A, Dreuw A, Wesolowski TA. Benchmark of the Extension of Frozen-Density Embedding Theory to Nonvariational Correlated Methods: The Embedded-MP2 Case. J Chem Theory Comput 2021; 17:4049-4062. [PMID: 34137597 DOI: 10.1021/acs.jctc.1c00228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The extension of the frozen-density embedding theory for nonvariational methods [J. Chem. Theory Comput. 2020, 16, 6880] was utilized to evaluate intermolecular interaction energies for complexes in the Zhao-Truhlar basis set. In the applied method (FDET-MP2-FAT-LDA), the same auxiliary system is used to evaluate the correlation energy by means of the second-order Møller-Plesset perturbation theory (MP2), as in our previous work [J. Chem. Phys. 2019, 150, 121101]. Local density approximation is used for ExcTnad[ρA,ρB] in both cases. Additionally, the contribution to the energy due to the neglected correlation potential was evaluated and analyzed. The domain of applicability of the local density approximation for ExcTnad[ρA,ρB] was determined based on deviations from the interaction energies from the conventional MP2 calculations. The local density approximation for ExcTnad[ρA,ρB] performs well for hydrogen- or dipole-bound complexes. The relative errors in the interaction energy lie within 3-30%. While for charge-transfer complexes, this approximation fails consistently, and for other types of complexes, the performance of this approximation is not systematic. The sources of error are discussed in detail.
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Affiliation(s)
- Reena Sen
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University Heidelberg, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | | | - Alexander Zech
- Department of Physical Chemistry, University of Geneva, 30, Quai Ernest-Ansermet, CH-1211 Genève 4, Switzerland
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University Heidelberg, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Tomasz A Wesolowski
- Department of Physical Chemistry, University of Geneva, 30, Quai Ernest-Ansermet, CH-1211 Genève 4, Switzerland
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26
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Gromov OI. Performance of the DLPNO-CCSD and recent DFT methods in the calculation of isotropic and dipolar contributions to 14N hyperfine coupling constants of nitroxide radicals. J Mol Model 2021; 27:194. [PMID: 34075533 DOI: 10.1007/s00894-021-04807-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/26/2021] [Indexed: 10/21/2022]
Abstract
In the present study, the performance of a set of density functionals: BP86, PBE, OLYP, BEEF, PBEpow, TPSS, SCAN, PBEGXPBE, M06L, MN15L, B3LYP, PBE0, mPW1PW, B97, BHandHLYP, mPW1PW, B98, TPSS0, PBE1KCIS, SCAN0, M06, M06-2X, MN15, CAM-B3LYP, ωB97x, B2PLYP, and the B3LYP/N07D and PBE/N07D schemes in the calculation of the 14N anisotropic hyperfine coupling (HFC) constants of a set of 23 nitroxide radicals is evaluated. The results are compared with those obtained with the DLPNO-CCSD method and experimental HFC values. Harmonic contribution to the 14N HFC vibrational correction was calculated at the revPBE0/def2-TZVPP level and included in the evaluation. With the vibrational correction, the DLPNO-CCSD method yielded HFC values in good agreement with the experiment (mean absolute deviation (MAD) = 0.3 G for the dipole-dipole contribution and MAD = 0.8 G for the contact coupling contribution). The best DFT results are obtained using the M06 functional with MAD = 0.2 G for the dipole-dipole contribution and MAD = 0.7 G for the contact coupling contribution. In general, vibrational correction significantly improved most DFT functionals' performance but did not change its overall ranking.
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Affiliation(s)
- Oleg I Gromov
- Chemistry Department, Lomonosov Moscow State University, Leninskiye Gory 1-3, Moscow, 119991, Russia.
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27
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Daas T, Fabiano E, Della Sala F, Gori-Giorgi P, Vuckovic S. Noncovalent Interactions from Models for the Møller-Plesset Adiabatic Connection. J Phys Chem Lett 2021; 12:4867-4875. [PMID: 34003655 PMCID: PMC8280728 DOI: 10.1021/acs.jpclett.1c01157] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 05/13/2021] [Indexed: 05/08/2023]
Abstract
Given the omnipresence of noncovalent interactions (NCIs), their accurate simulations are of crucial importance across various scientific disciplines. Here we construct accurate models for the description of NCIs by an interpolation along the Møller-Plesset adiabatic connection (MP AC). Our interpolation approximates the correlation energy, by recovering MP2 at small coupling strengths and the correct large-coupling strength expansion of the MP AC, recently shown to be a functional of the Hartree-Fock density. Our models are size consistent for fragments with nondegenerate ground states, have the same cost as double hybrids, and require no dispersion corrections to capture NCIs accurately. These interpolations greatly reduce large MP2 errors for typical π-stacking complexes (e.g., benzene-pyridine dimers) and for the L7 data set. They are also competitive with state-of-the-art dispersion enhanced functionals and can even significantly outperform them for a variety of data sets, such as CT7 and L7.
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Affiliation(s)
- Timothy
J. Daas
- Department
of Chemistry & Pharmaceutical Sciences and Amsterdam Institute
of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
| | - Eduardo Fabiano
- Institute
for Microelectronics and Microsystems (CNR-IMM), Via Monteroni, Campus Unisalento, 73100 Lecce, Italy
- Center
for Biomolecular Nanotechnologies, Istituto
Italiano di Tecnologia, Via Barsanti 14, 73010 Arnesano (LE), Italy
| | - Fabio Della Sala
- Institute
for Microelectronics and Microsystems (CNR-IMM), Via Monteroni, Campus Unisalento, 73100 Lecce, Italy
- Center
for Biomolecular Nanotechnologies, Istituto
Italiano di Tecnologia, Via Barsanti 14, 73010 Arnesano (LE), Italy
| | - Paola Gori-Giorgi
- Department
of Chemistry & Pharmaceutical Sciences and Amsterdam Institute
of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
| | - Stefan Vuckovic
- Department
of Chemistry & Pharmaceutical Sciences and Amsterdam Institute
of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
- Physical
and Theoretical Chemistry, University of
Saarland, 66123 Saarbrücken, Germany
- Department
of Chemistry, University of California, Irvine, California 92697, United States
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28
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Loos PF, Comin M, Blase X, Jacquemin D. Reference Energies for Intramolecular Charge-Transfer Excitations. J Chem Theory Comput 2021; 17:3666-3686. [DOI: 10.1021/acs.jctc.1c00226] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Pierre-François Loos
- Laboratoire de Chimie et Physique Quantiques, Université de Toulouse, CNRS, UPS, F-31400 Toulouse, France
| | | | - Xavier Blase
- Univ. Grenoble Alpes, CNRS, Inst NEEL, F-38042 Grenoble, France
| | - Denis Jacquemin
- Université de Nantes, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
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29
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Unprecedented saturation limit achieved by inorganic polycationic cluster (Sb 7Te 8) 5+ for light noble gases (He & Ne). J Mol Graph Model 2021; 106:107910. [PMID: 33848947 DOI: 10.1016/j.jmgm.2021.107910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/20/2021] [Accepted: 03/24/2021] [Indexed: 11/22/2022]
Abstract
Among noble gases, Helium and Neon have smaller size, high ionization potential and low polarizability due to which these two gases exhibit weak binding affinities toward any surface. Bartlet's discovery and subsequent similar successful discoveries of stable complexes of noble gases opened new avenues for the storage of noble gases particularly on the new surfaces and their interactions for the storage of these gases. Here, we report the adsorption of light noble gases on polycationic clusters. Our current work not only investigates the interaction behavior of He and Ne with (Sb7Te8)5+ cluster but also explores the saturation limit of the cluster for He and Ne. Stability of various complexes of He and Ne with cationic surfaces is determined by the calculation of their interaction energies which reveal that the adsorption of single and multiple atoms of noble gases at faces of double cubic cluster is comparatively more favorable than at the bond lengths. Electronic properties such as HOMO-LUMO gaps show that complexes of He and Ne are more stable electronically than that of pure cluster, because HOMO-LUMO gap of complexes are higher than the bare polycationic cluster. NCI analysis of iso-surfaces and RDG maps confirms the presence of van der Waals forces between light noble gases and polycationic clusters. Saturation studies reveal that cluster can adsorb eleven He and/or ten Ne atoms with no or minimum distortion in the geometry of cluster. The results showed that Ne has greater tendency to interact with polycationic clusters due to the large electronic cloud and polarizability value than He.
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30
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Błasiak B, Bednarska JD, Chołuj M, Góra RW, Bartkowiak W. Ab initio effective one-electron potential operators: Applications for charge-transfer energy in effective fragment potentials. J Comput Chem 2021; 42:398-411. [PMID: 33349929 DOI: 10.1002/jcc.26462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 11/18/2020] [Indexed: 12/19/2022]
Abstract
The concept of effective one-electron potentials (EOPs) has proven to be extremely useful in efficient description of electronic structure of chemical systems, especially extended molecular aggregates such as interacting molecules in condensed phases. Here, a general method for EOP-based elimination of electron repulsion integrals is presented, that is tuned toward the fragment-based calculation methodologies such as the second generation of the effective fragment potentials (EFP2) method. Two general types of the EOP operator matrix elements are distinguished and treated either via the distributed multipole expansion or the extended density fitting (DF) schemes developed in this work. The EOP technique is then applied to reduce the high computational costs of the effective fragment charge-transfer (CT) terms being the bottleneck of EFP2 potentials. The alternative EOP-based CT energy model is proposed, derived within the framework of intermolecular perturbation theory with Hartree-Fock noninteracting reference wavefunctions, compatible with the original EFP2 formulation. It is found that the computational cost of the EFP2 total interaction energy calculation can be reduced by up to 38 times when using the EOP-based formulation of CT energy, as compared to the original EFP2 scheme, without compromising the accuracy for a wide range of weakly interacting neutral and ionic molecular fragments. The proposed model can thus be used routinely within the EFP2 framework.
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Affiliation(s)
- Bartosz Błasiak
- Department of Physical and Quantum Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Joanna D Bednarska
- Department of Physical and Quantum Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Marta Chołuj
- Department of Physical and Quantum Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Robert W Góra
- Department of Physical and Quantum Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Wojciech Bartkowiak
- Department of Physical and Quantum Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
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31
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Jedwabny W, Dyguda-Kazimierowicz E, Pernal K, Szalewicz K, Patkowski K. Extension of an Atom-Atom Dispersion Function to Halogen Bonds and Its Use for Rational Design of Drugs and Biocatalysts. J Phys Chem A 2021; 125:1787-1799. [PMID: 33620223 PMCID: PMC8028329 DOI: 10.1021/acs.jpca.0c11347] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/10/2021] [Indexed: 12/17/2022]
Abstract
A dispersion function Das in the form of a damped atom-atom asymptotic expansion fitted to ab initio dispersion energies from symmetry-adapted perturbation theory was improved and extended to systems containing heavier halogen atoms. To illustrate its performance, the revised Das function was implemented in the multipole first-order electrostatic and second-order dispersion (MED) scoring model. The extension has allowed applications to a much larger set of biocomplexes than it was possible with the original Das. A reasonable correlation between MED and experimentally determined inhibitory activities was achieved in a number of test cases, including structures featuring nonphysically shortened intermonomer distances, which constitute a particular challenge for binding strength predictions. Since the MED model is also computationally efficient, it can be used for reliable and rapid assessment of the ligand affinity or multidimensional scanning of amino acid side-chain conformations in the process of rational design of novel drugs or biocatalysts.
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Affiliation(s)
- Wiktoria Jedwabny
- Department
of Chemistry, Wrocław University of
Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Edyta Dyguda-Kazimierowicz
- Department
of Chemistry, Wrocław University of
Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Katarzyna Pernal
- Institute
of Physics, Łódź University
of Technology, Wólczańska
219, 90-924 Łódź, Poland
| | - Krzysztof Szalewicz
- Department
of Physics and Astronomy, University of
Delaware, Newark, Delaware 19716, United
States
| | - Konrad Patkowski
- Department
of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
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32
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Alkali Metal Doping for Enhancement of Nonlinear Optical Properties of Dicyclopenta[4,3,2,1-ghi:4′,3′,2′,1′-pqr]perylene: A New Bowl-Shaped Fragment of Fullerene C70. J Inorg Organomet Polym Mater 2021. [DOI: 10.1007/s10904-020-01715-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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33
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Fuhrer TJ, Snelgrove J, Corley CA, Iacono ST. Density Functional Theory Investigation of Fulvene-Derivatized Fullerenes as Candidates for Organic Solar Cells. J Phys Chem A 2020; 124:10324-10329. [PMID: 33228357 DOI: 10.1021/acs.jpca.0c06469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Interest within the scientific community in organic solar cells has been on the rise over the last two decades as researchers respond to increasing demands for alternative renewable energy sources. Fulvene, fullerene, and endohedral metallofullerene derivatives have individually shown great promise as efficient charge transfer agents. Despite the heavy demand for research in this area, there have been no studies reported to date that explore the electronic behavior of molecules containing both fullerene and fulvene groups. The lack of interest may be attributed to inherent limitations and inaccuracy in most density functional theory (DFT) band gap calculations for large molecules. Herein we present a systematic computational investigation of the band gaps and dipole moments of several test fullerene-fulvene molecules using a novel DFT method that has been modified to allow accurate computation of the band gaps of this class of molecules. Calculated results showed promising low band gap energies and attractive conductive properties for all fullerene-fulvene derivatives. This new DFT method can conceivably be an invaluable tool that can provide predictive insight into the suitability of similar high molecular weight materials for application in organic solar cell devices.
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Affiliation(s)
- Timothy J Fuhrer
- Department of Chemistry, Radford University, Radford, Virginia 24142, United States
| | - Jordan Snelgrove
- Department of Chemistry, Radford University, Radford, Virginia 24142, United States
| | - Cynthia A Corley
- Department of Chemistry and Chemistry Research Center, United States Air Force Academy, Colorado Springs, Colorado 80840, United States
| | - Scott T Iacono
- Department of Chemistry and Chemistry Research Center, United States Air Force Academy, Colorado Springs, Colorado 80840, United States
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34
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Jana S, Śmiga S, Constantin LA, Samal P. Generalizing Double-Hybrid Density Functionals: Impact of Higher-Order Perturbation Terms. J Chem Theory Comput 2020; 16:7413-7430. [PMID: 33205659 PMCID: PMC7735712 DOI: 10.1021/acs.jctc.0c00823] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Indexed: 11/28/2022]
Abstract
Connections between the Görling-Levy (GL) perturbation theory and the parameters of double-hybrid (DH) density functional are established via adiabatic connection formalism. Moreover, we present a more general DH density functional theory, where the higher-order perturbation terms beyond the second-order GL2 one, such as GL3 and GL4, also contribute. It is shown that a class of DH functionals including previously proposed ones can be formed using the present construction. Based on the proposed formalism, we assess the performance of higher-order DH and long-range corrected DH formed on the Perdew-Burke-Ernzerhof (PBE) semilocal functional and second-order GL2 correlation energy. The underlying construction of DH functionals based on the generalized many-body perturbation approaches is physically appealing in terms of the development of the non-local forms using more accurate and sophisticated semilocal functionals.
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Affiliation(s)
- Subrata Jana
- School
of Physical Sciences, National Institute
of Science Education and Research, HBNI, Bhubaneswar 752050, India
| | - Szymon Śmiga
- Institute
of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Toruń, Poland
| | - Lucian A. Constantin
- Consiglio
Nazionale delle Ricerche CNR-NANO, Istituto
di Nanoscienze, 41125 Modena, Italy
| | - Prasanjit Samal
- School
of Physical Sciences, National Institute
of Science Education and Research, HBNI, Bhubaneswar 752050, India
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35
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Computational Investigations of Dispersion Interactions between Small Molecules and Graphene-like Flakes. J Phys Chem A 2020; 124:9552-9561. [PMID: 33166136 DOI: 10.1021/acs.jpca.0c06595] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We investigate dispersion interactions in a selection of atomic, molecular, and molecule-surface systems, comparing high-level correlated methods with empirically corrected density functional theory (DFT). We assess the efficacy of functionals commonly used for surface-based calculations, with and without the D3 correction of Grimme. We find that the inclusion of the correction is essential to get meaningful results, but there is otherwise little to distinguish between the functionals. We also present coupled-cluster quality interaction curves for H2, NO2, H2O, and Ar interacting with large carbon flakes, acting as models for graphene surfaces, using novel absolutely localized molecular orbital based methods. These calculations demonstrate that the problems with empirically corrected DFT when investigating dispersion appear to compound as the system size increases, with important implications for future computational studies of molecule-surface interactions.
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36
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Patra A, Jana S, Samal P. A way of resolving the order-of-limit problem of Tao–Mo semilocal functional. J Chem Phys 2020; 153:184112. [DOI: 10.1063/5.0025173] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Abhilash Patra
- School of Physical Sciences, National Institute of Science Education and Research, HBNI, Bhubaneswar 752050, India
| | - Subrata Jana
- School of Physical Sciences, National Institute of Science Education and Research, HBNI, Bhubaneswar 752050, India
| | - Prasanjit Samal
- School of Physical Sciences, National Institute of Science Education and Research, HBNI, Bhubaneswar 752050, India
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37
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Santos GFN, Carvalho LC, Oliveira DAS, Rego DG, Bueno MA, Oliveira BG. The definitive challenge of forming uncommon pseudo‐π···H–F and C···H–F hydrogen bonds on cyclic and cubic nonpolar hydrocarbons. J PHYS ORG CHEM 2020. [DOI: 10.1002/poc.4098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Leila Cardoso Carvalho
- Centro das Ciências Exatas e das Tecnologias Universidade Federal do Oeste da Bahia Barreiras Brazil
| | | | - Danilo Guimarães Rego
- Centro das Ciências Exatas e das Tecnologias Universidade Federal do Oeste da Bahia Barreiras Brazil
| | - Mauro Alves Bueno
- Centro das Ciências Exatas e das Tecnologias Universidade Federal do Oeste da Bahia Barreiras Brazil
| | - Boaz Galdino Oliveira
- Centro das Ciências Exatas e das Tecnologias Universidade Federal do Oeste da Bahia Barreiras Brazil
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38
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Melancon KM, Cundari TR. Computational investigations of NHC-backbone configurations for applications in organocatalytic umpolung reactions. Org Biomol Chem 2020; 18:7437-7447. [PMID: 32940280 DOI: 10.1039/d0ob01267j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Density functional theory (DFT) and multiconfigurational self-consistent field theory (MCSCF) methods are employed to investigate variation of the electronic properties of various N-heterocyclic carbenes. Alterations to the backbone by increased or decreased conjugation, heteroatom substitution in the NHC ring, and electron-donating or -withdrawing backbone substituents are modeled. The MCSCF calculations show extensive delocalization of both the highest occupied and lowest unoccupied molecular orbitals for NHCs with polymerizable backbone substituents. The free energies of the intermediates and transition structures for benzoin condensation are also shown to be sensitive to substitution of the NHC backbone. Taken together, these results imply great sensitivity of the reactivity of poly(NHC) catalysts to backbone modification at this moiety. Implications with respect to enhancement of poly(NHC)s employed in umpolung catalysis are discussed.
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Affiliation(s)
- Kortney M Melancon
- University of North Texas, Department of Chemistry, Denton, Texas 76201, USA.
| | - Thomas R Cundari
- University of North Texas, Department of Chemistry, Denton, Texas 76201, USA.
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39
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Molecular interactions in 2-hydroxyethyl-trimethylammonium acetate (choline acetate) ion pair. J CHEM SCI 2020. [DOI: 10.1007/s12039-020-01800-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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40
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Śmiga S, Constantin LA. Modified Interaction-Strength Interpolation Method as an Important Step toward Self-Consistent Calculations. J Chem Theory Comput 2020; 16:4983-4992. [PMID: 32559078 PMCID: PMC7588043 DOI: 10.1021/acs.jctc.0c00328] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The modified point charge plus continuum (mPC) model [ConstantinL. A.; 2019, 99, 085117] solves
the important failures of the original counterpart, namely, the divergences
when the reduced gradient of the density is large, such as in the
tail of the density and in quasi-dimensional density regimes. The
mPC allows us to define a modified interaction-strength interpolation
(mISI) method inheriting these good features, which are important
steps toward the full self-consistent treatment. Here, we provide
an assessment of mISI for molecular systems (i.e.,
considering thermochemistry properties, correlation energies, vertical
ionization potentials, and several noncovalent interactions), harmonium
atoms, and functional derivatives in the strong-interaction limit.
For all our tests, mISI provides a systematic improvement over the
original ISI method. Semilocal approximations of the second-order
Görling–Levy (GL2) perturbation theory are also considered
in the mISI method, showing considerable worsening of the results.
Possible further development of mISI is briefly discussed.
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Affiliation(s)
- Szymon Śmiga
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, 87-100 Toruń, Poland
| | - Lucian A Constantin
- Consiglio Nazionale delle Ricerche CNR-NANO, Istituto di Nanoscienze, 41125 Modena, Italy
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41
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Zhang IY, Xu X. On the top rung of Jacob's ladder of density functional theory: Toward resolving the dilemma of
SIE
and
NCE. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1490] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Igor Ying Zhang
- Shanghai Key Laboratory of Molecular Catalysis and Innovation Materials, Collaborative Innovation Centre of Chemistry for Energy Materials, MOE Laboratory for Computational Physical Science, Department of Chemistry Fudan University Shanghai China
| | - Xin Xu
- Shanghai Key Laboratory of Molecular Catalysis and Innovation Materials, Collaborative Innovation Centre of Chemistry for Energy Materials, MOE Laboratory for Computational Physical Science, Department of Chemistry Fudan University Shanghai China
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42
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Yu F, Wang Y. Dual‐hybrid direct random phase approximation and second‐order screened exchange with nonlocal van der Waals correlations for noncovalent interactions. J Comput Chem 2020; 41:1018-1025. [DOI: 10.1002/jcc.26149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/05/2020] [Accepted: 01/06/2020] [Indexed: 11/09/2022]
Affiliation(s)
- Feng Yu
- Department of Physics, School of ScienceXi'an Technological University Xi'an Shaanxi China
| | - Yaoting Wang
- Department of Physics, School of ScienceXi'an Technological University Xi'an Shaanxi China
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44
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Bandyopadhyay P, Karmakar A, Deb J, Sarkar U, Seikh MM. Non-covalent interactions between epinephrine and nitroaromatic compounds: A DFT study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 228:117827. [PMID: 31787535 DOI: 10.1016/j.saa.2019.117827] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 11/17/2019] [Accepted: 11/18/2019] [Indexed: 06/10/2023]
Abstract
Here, we present a density functional theory (DFT) study of hydrogen bonding and π-π stacking interactions between epinephrine and different aromatic nitro-compounds in gas phase as well as in methanol solvent. Detail investigations of hydrogen bonding and π-π interactions are performed and confirmed on the basis of theoretical IR spectra, natural bond orbital (NBO) analysis, non-covalent interaction (NCI), chemical reactivity descriptors and electronic spectra. Among different functionals used for the calculation, the results obtained from ωB97XD functional are found to be more suitable to describe the hydrogen bonding and π-π stacking phenomenon for our considered systems. Weakening of hydrogen bonding and π-π stacking interaction on solvent incorporation is observed. Electronic transition between different orbitals and transition probabilities of epinephrine and nitro-aromatic complexes are described using time dependent density functional theory (TD-DFT) method.
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Affiliation(s)
- Prasanta Bandyopadhyay
- Department of Chemistry, Visva-Bharati University, Santiniketan 731235, West Bengal, India.
| | - Animesh Karmakar
- Department of Chemistry, Visva-Bharati University, Santiniketan 731235, West Bengal, India
| | - Jyotirmoy Deb
- Department of Physics, Assam University, Silchar 788011, India
| | - Utpal Sarkar
- Department of Physics, Assam University, Silchar 788011, India
| | - Md Motin Seikh
- Department of Chemistry, Visva-Bharati University, Santiniketan 731235, West Bengal, India.
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45
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Chen JL, Sun T, Wang YB, Wang W. Toward a less costly but accurate calculation of the CCSD(T)/CBS noncovalent interaction energy. J Comput Chem 2020; 41:1252-1260. [PMID: 32045021 DOI: 10.1002/jcc.26171] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 01/12/2020] [Accepted: 02/01/2020] [Indexed: 01/14/2023]
Abstract
The popular method of calculating the noncovalent interaction energies at the coupled-cluster single-, double-, and perturbative triple-excitations [CCSD(T)] theory level in the complete basis set (CBS) limit was to add a CCSD(T) correction term to the CBS second-order Møller-Plesset perturbation theory (MP2). The CCSD(T) correction term is the difference between the CCSD(T) and MP2 interaction energies evaluated in a medium basis set. However, the CCSD(T) calculations with the medium basis sets are still very expensive for systems with more than 30 atoms. Comparatively, the domain-based local pair natural orbital coupled-cluster method [DLPNO-CCSD(T)] can be applied to large systems with over 1,000 atoms. Considering both the computational accuracy and efficiency, in this work, we propose a new scheme to calculate the CCSD(T)/CBS interaction energies. In this scheme, the MP2/CBS term keeps intact and the CCSD(T) correction term is replaced by a DLPNO-CCSD(T) correction term which is the difference between the DLPNO-CCSD(T) and DLPNO-MP2 interaction energies evaluated in a medium basis set. The interaction energies of the noncovalent systems in the S22, HSG, HBC6, NBC10, and S66 databases were recalculated employing this new scheme. The consistent and tight settings of the truncation parameters for DLPNO-CCSD(T) and DLPNO-MP2 in this noncanonical CCSD(T)/CBS calculations lead to the maximum absolute deviation and root-mean-square deviation from the canonical CCSD(T)/CBS interaction energies of less than or equal to 0.28 kcal/mol and 0.09 kcal/mol, respectively. The high accuracy and low cost of this new computational scheme make it an excellent candidate for the study of large noncovalent systems.
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Affiliation(s)
- Jiu-Li Chen
- Department of Chemistry, and Key Laboratory of Guizhou High Performance Computational Chemistry, Guizhou University, Guiyang, China
| | - Tao Sun
- Department of Chemistry, and Key Laboratory of Guizhou High Performance Computational Chemistry, Guizhou University, Guiyang, China
| | - Yi-Bo Wang
- Department of Chemistry, and Key Laboratory of Guizhou High Performance Computational Chemistry, Guizhou University, Guiyang, China
| | - Weizhou Wang
- College of Chemistry and Chemical Engineering, and Henan Key Laboratory of Function-Oriented Porous Materials, Luoyang Normal University, Luoyang, China
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46
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Wang Y, Verma P, Zhang L, Li Y, Liu Z, Truhlar DG, He X. M06-SX screened-exchange density functional for chemistry and solid-state physics. Proc Natl Acad Sci U S A 2020; 117:2294-2301. [PMID: 31953258 PMCID: PMC7007546 DOI: 10.1073/pnas.1913699117] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Screened-exchange hybrid density functionals are especially recommended for solid-state systems because they combine the advantages of hybrid functionals with the correct physics and lower computational cost associated with the attenuation of Hartree-Fock exchange at long range. We present a screened-exchange hybrid functional, M06-SX, that combines the functional form of the local revM06-L functional with a percentage of short-range nonlocal Hartree-Fock exchange. The M06-SX functional gives good results not only for a large set of training data but also for several databases quite different from the training data. The mean unsigned error (MUE) of the M06-SX functional is 2.85 kcal/mol for 418 atomic and molecular energies (AME418) in Minnesota Database 2019, which is better than all five other screened-exchange hybrid functionals tested in this work. The M06-SX functional also gives especially good results for semiconductor band gaps, molecular dissociation energies, noncovalent interactions, barrier heights, and electronic excitation energies excluding long-range charge transfer excitations. For the LC18 lattice constants database, the M06-SX functional gives an MUE of only 0.034 Å. Therefore, the M06-SX functional is well suited for studying molecular chemistry as well as solid-state physics.
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Affiliation(s)
- Ying Wang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410006, China
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Pragya Verma
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455-0431
- Chemical Theory Center, University of Minnesota, Minneapolis, MN 55455-0431
- Nanoporous Materials Genome Center, University of Minnesota, Minneapolis, MN 55455-0431
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455-0431
| | - Lujia Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai 200062, China
| | - Yaqi Li
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410006, China
| | - Zhonghua Liu
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410006, China
| | - Donald G Truhlar
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455-0431;
- Chemical Theory Center, University of Minnesota, Minneapolis, MN 55455-0431
- Nanoporous Materials Genome Center, University of Minnesota, Minneapolis, MN 55455-0431
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455-0431
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China;
- New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai 200062, China
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47
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Verma PL, Gejji SP. Electronic structure, vibrational spectra and 1H NMR chemical shifts of the ion pair composites within imidazolium functionalized geminal dicationic ionic liquids from density functional theory. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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48
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Garcia J, Szalewicz K. Ab Initio Extended Hartree-Fock plus Dispersion Method Applied to Dimers with Hundreds of Atoms. J Phys Chem A 2020; 124:1196-1203. [PMID: 31961678 DOI: 10.1021/acs.jpca.9b11900] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Hartree-Fock plus dispersion plus first-order correlation (HFDc(1)) method consists in augmenting the HF interaction energy by the correlation part of the first-order interaction energy and the second-order dispersion and exchange-dispersion energies. All of the augmentation terms are computed using the symmetry-adapted perturbation theory based on density functional theory description of monomers [SAPT(DFT)]; thus, HFDc(1) is a fully ab initio method. A partly empirical version of this method, HFDasc(1), uses a damped asymptotic expansion for the dispersion plus exchange-dispersion term fitted to SAPT(DFT) ab initio values. The HFDc(1) interaction energies for dimers in the S22, S66, S66x8, NCCE31, IonHB, and UD-ARL benchmark data sets are more accurate than those given by most ab initio methods with comparable costs. HFDc(1) can be used routinely for dimers with nearly 200 atoms, such as included in the S12L benchmark set, giving results comparable to those obtained by the most expensive methods applicable.
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Affiliation(s)
- Javier Garcia
- Department of Physics and Astronomy , University of Delaware , Newark , Delaware 19716 , United States
| | - Krzysztof Szalewicz
- Department of Physics and Astronomy , University of Delaware , Newark , Delaware 19716 , United States
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Clarke SM, Steele BA, Kroonblawd MP, Zhang D, Kuo IFW, Stavrou E. An Isosymmetric High-Pressure Phase Transition in α-Glycylglycine: A Combined Experimental and Theoretical Study. J Phys Chem B 2020; 124:1-10. [PMID: 31794209 DOI: 10.1021/acs.jpcb.9b07313] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We investigated the effects of hydrostatic pressure on α-glycylglycine (α-digly) using a combined experimental and theoretical approach. The results of powder X-ray diffraction show a change in compressibility of the axes above 6.7 GPa, but also indicate that the structure remains in the same monoclinic space group, suggesting an isosymmetric phase transition. A noticeable change in the Raman spectra between 6 and 7.5 GPa further supports the observed phase transition. First-principles-based calculations combined with the crystal structure prediction code USPEX predict a number of possible polymorphs at high pressure. An orthorhombic structure with a bent peptide backbone is the lowest enthalpy polymorph above 6.4 GPa; however, it is not consistent with experimental observations. A second monoclinic structure isosymmetric to α-digly, α'-digly, is predicted to become more stable above 11.4 GPa. The partial atomic charges in α'-digly differ from α-digly, and the molecule is bent, possibly indicating different reactivity of α'-digly. The similarity in the lattice parameters predicted from calculations and the axial changes observed experimentally support that the α'-digly phase is likely observed at high pressure. A possible explanation for the isosymmetric phase transition is discussed in terms of relaxing strained hydrogen bonding interactions. Such combined experimental and modeling efforts provide atomic-level insight into how pressure-driven conformational changes alter hydrogen-bonding networks in complicated molecular crystals.
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Affiliation(s)
- Samantha M Clarke
- Physical and Life Sciences Directorate , Lawrence Livermore National Laboratory , P.O. Box 808, Livermore , California 94550 , United States
| | - Brad A Steele
- Physical and Life Sciences Directorate , Lawrence Livermore National Laboratory , P.O. Box 808, Livermore , California 94550 , United States
| | - Matthew P Kroonblawd
- Physical and Life Sciences Directorate , Lawrence Livermore National Laboratory , P.O. Box 808, Livermore , California 94550 , United States
| | - Dongzhou Zhang
- Partnership for Extreme Crystallography, University of Hawaii at Manoa , Argonne , Illinois 60439 , United States
| | - I-Feng W Kuo
- Physical and Life Sciences Directorate , Lawrence Livermore National Laboratory , P.O. Box 808, Livermore , California 94550 , United States
| | - Elissaios Stavrou
- Physical and Life Sciences Directorate , Lawrence Livermore National Laboratory , P.O. Box 808, Livermore , California 94550 , United States
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Arabi AA. Binding energies of van der Waals complexes at non-equilibrium geometries. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2019.110545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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