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Ahirwar MB, Gadre SR, Deshmukh MM. Molecular Tailoring Approach for the Direct Estimation of Individual Noncovalent Interaction Energies in Molecular Systems. J Phys Chem A 2024; 128:6099-6115. [PMID: 39037864 DOI: 10.1021/acs.jpca.4c01176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
The noncovalent interactions (NCIs) are omnipresent in chemistry, physics, and biology. The study of such interactions offers insights into various physicochemical phenomena. Some indirect approaches proposed in the literature for exploring the NCIs are briefly reviewed in Section 1 of this Perspective. These include: (i) Shift in the stretching frequency of an X-Y bond involved in X-Y···Z interaction. (ii) Topological analysis of molecular electron density. (iii) Empirical equations derived employing experimental and theoretical quantities. However, a direct method for estimating individual intramolecular/intermolecular interaction energies has been conspicuous by its absence from the literature. We have developed a molecular tailoring approach (MTA)-based method enabling a direct and reliable estimation of the energy of intra- as well as intermolecular interactions. This method offers a direct and reliable estimation of these interactions, in particular of the hydrogen bonds (HB) in molecules/weakly bound clusters along with the respective cooperativity contribution. In Section 2, the basis of our method is discussed, along with some illustrative examples. The application of this method to a variety of molecules and clusters, with a special emphasis on estimating the HB energy along with the energy of other NCIs is presented in Section 3. Section 4 discusses some computational strategies for applying our method to large molecular clusters. The last Section provides a summary and a discussion on future developments.
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Affiliation(s)
- Mini Bharati Ahirwar
- Department of Chemistry, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar 470003, India
| | - Shridhar R Gadre
- Department of Scientific Computing, Modelling, & Simulation, Savitribai Phule Pune University, Pune 411007, India
- Department of Chemistry, Savitribai Phule Pune University, Pune 411007, India
| | - Milind M Deshmukh
- Department of Chemistry, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar 470003, India
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2
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Del Angel Cruz D, Ferreras KN, Harville T, Schoendorff G, Gordon MS. Analysis of bonding motifs in unusual molecules I: planar hexacoordinated carbon atoms. Phys Chem Chem Phys 2024. [PMID: 39078376 DOI: 10.1039/d4cp01800a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
The bonding structures of CO3Li3+ and CS3Li3+ are studied by means of oriented quasi-atomic orbitals (QUAOs) to assess the possibility of these molecules being planar hexacoordinated carbon (phC) systems. CH3Li and CO32- are employed as reference molecules. It is found that the introduction of Li+ ions into the molecular environment of carbonate has a greater effect on the orbital structure of the O atoms than it does on the C atom. Partial charges computed from QUAO populations imply repulsion between the positively charged C and Li atoms in CO3Li3+. Upon the transition from CO3Li3+ to CS3Li3+, the analysis reveals that the substitution of O atoms by S atoms inverts the polarity of the carbon-chalcogen σ bond. This is linked to the difference in s- and p-fractions of the QUAOs of C and S, as element electronegativities do not explain the observed polarity of the CSσ bond. Partial charges indicate that the larger electron population on the C atom in CS3Li3+ makes C-Li attraction possible. Upon comparison with the C-Li bond in methyllithium, it is found that the C-Li covalent interactions in CO3Li3+ and CS3Li3+ have about 14% and 6% of the strength of the C-Li covalent interaction in CH3Li, respectively. Consequently, it is concluded that only CS3Li3+ may be considered to be a phC system.
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Affiliation(s)
- Daniel Del Angel Cruz
- Department of Chemistry and Ames National Laboratory, Iowa State University, Ames, Iowa, 50011, USA.
| | - Katherine N Ferreras
- Department of Chemistry and Ames National Laboratory, Iowa State University, Ames, Iowa, 50011, USA.
| | - Taylor Harville
- Department of Chemistry and Ames National Laboratory, Iowa State University, Ames, Iowa, 50011, USA.
| | - George Schoendorff
- Department of Chemistry, University of South Dakota, Vermillion, South Dakota, 57069, USA
| | - Mark S Gordon
- Department of Chemistry and Ames National Laboratory, Iowa State University, Ames, Iowa, 50011, USA.
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3
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Guidez EB. Quasi-atomic orbital analysis of halogen bonding interactions. J Chem Phys 2023; 159:194307. [PMID: 37987522 DOI: 10.1063/5.0174171] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023] Open
Abstract
A quasi-atomic orbital analysis of the halogen bonded NH3⋯XF complexes (X = F, Cl, Br, and I) is performed to gain insight into the electronic properties associated with these σ-hole interactions. It is shown that significant sharing of electrons between the nitrogen lone pair of the ammonia molecule and the XF molecule occurs, resulting in a weakening of the X-F bond. In addition, the N-X bond shows increasing covalent character as the size of the halogen atom X increases. While the Mulliken outer complex NH3⋯XF appears to be overall the main species, the strength of the covalent interaction of the N-X bond becomes increasingly similar to that of the N-X bond in the [NH3X]+ cation as the size of X increases.
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Affiliation(s)
- Emilie B Guidez
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217, USA
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4
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Kim S, Conrad JA, Tow GM, Maginn EJ, Boatz JA, Gordon MS. Intermolecular interactions in clusters of ethylammonium nitrate and 1-amino-1,2,3-triazole. Phys Chem Chem Phys 2023; 25:30428-30457. [PMID: 37917371 DOI: 10.1039/d3cp02407e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
The intermolecular interaction energies, including hydrogen bonds (H-bonds), of clusters of the ionic liquid ethylammonium nitrate (EAN) and 1-amino-1,2,3-triazole (1-AT) based deep eutectic propellants (DeEP) are examined. 1-AT is introduced as a neutral hydrogen bond donor (HBD) to EAN in order to form a eutectic mixture. The effective fragment potential (EFP) is used to examine the bonding interactions in the DeEP clusters. The resolution of the Identity (RI) approximated second order Møller-Plesset perturbation theory (RI-MP2) and coupled cluster theory (RI-CCSD(T)) are used to validate the EFP results. The EFP method predicts that there are significant polarization and charge transfer effects in the EAN:1-AT complexes, along with Coulombic, dispersion and exchange repulsion interactions. The EFP interaction energies are in good agreement with the RI-MP2 and RI-CCSD(T) results. The quasi-atomic orbital (QUAO) bonding and kinetic bond order (KBO) analyses are additionally used to develop a conceptual and semi-quantitative understanding of the H-bonding interactions as a function of the size of the system. The QUAO and KBO analyses suggest that the H-bonds in the examined clusters follow the characteristic hydrogen bonding three-center four electron interactions. The strongest H-bonding interactions between the (EAN)1:(1-AT)n and (EAN)2:(1-AT)n (n = 1-5) complexes are observed internally within EAN; that is, between the ethylammonium cation [EA]+ and the nitrate anion ([NO3]-). The weakest H-bonding interactions occur between [NO3]- and 1-AT. Consequently, the average strengths of the H-bonds within a given (EAN)x:(1-AT)n complex decrease as more 1-AT molecules are introduced into the EAN monomer and EAN dimer. The QUAO bonding analysis suggests that 1-AT in (EAN)x:(1-AT)n can act as both a HBD and a hydrogen bond acceptor simultaneously. It is observed that two 1-AT molecules can form H-bonds to each other. Although the KBOs that correspond to H-bonding interactions in [EA]+:1-AT, [NO3]-:1-AT and between two 1-AT molecules are weaker than the H-bonds in EAN, those weak H-bond networks with 1-AT could be important to form a stable DeEP.
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Affiliation(s)
- Shinae Kim
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, IA 50011, USA.
- Combustion Research Facility, Sandia National Laboratories, Livermore, California 94550, USA
| | - Justin A Conrad
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, IA 50011, USA.
| | - Garrett M Tow
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Edward J Maginn
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Jerry A Boatz
- Aerospace Systems Directorate, Air Force Research Laboratory, Edwards Air Force Base, California 93524, USA
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, IA 50011, USA.
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5
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Del Angel Cruz D, Galvez Vallejo JL, Gordon MS. Analysis of the bonding in tetrahedrane and phosphorus-substituted tetrahedranes. Phys Chem Chem Phys 2023; 25:27276-27292. [PMID: 37791459 DOI: 10.1039/d3cp03619g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The bonding structures of tetrahedrane, phosphatetrahedrane, diphosphatetrahedrane and triphosphatetrahedrane are studied by employing an intrinsic quasi-atomic orbital analysis. Ethane, cyclopropane and tetrahedral P4 are employed as reference systems. The orbital analysis is paired with the computation of strain energies via isodesmic reactions. The results show that the increase in geometric strain upon transition from ethane to cyclopropane to tetrahedrane weakens the CC bonds, despite leading to shorter C-C interatomic distances. With the increase in strain, the orbitals centered on C and involved in the bonding of the cage structure are observed to have elevated p-character, and the orbital structure of C deviates from sp3 hybridization. The systematic substitution of CH groups by P atoms in the cage structure of tetrahedrane leads to stronger CC bonds, larger angles in the cage structures of the resulting phosphatetrahedranes, lower p-character in the orbitals involved in the bonding of the cages, and lower strain energies. It is found that P is more amenable to strained molecular arrangements than is C, and that the propensity of a given atom to hybridize s and p functions, or the lack thereof, has implications in the stability of molecules with strained geometries. The combination of the calculations presented here with the existing literature provides insight into the apparent propensity of tetrahedrane and P4 to 'break' their tetrahedral structures. Trends in the bonding interactions, such as bond strengths, s- and p-orbital characters and charge transfer are identified and related to the strain energy observed in each of the analyzed systems.
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Affiliation(s)
| | - Jorge L Galvez Vallejo
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA.
- School of Computing, Australian National University, Canberra, ACT 2601, Australia
| | - Mark S Gordon
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA.
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6
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Varandas AJC. Carbon-[ n]Triangulenes and Sila-[ n]Triangulenes: Which Are Planar? J Phys Chem A 2023. [PMID: 37256705 DOI: 10.1021/acs.jpca.3c01820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Using our recently suggested concept of a quasi-molecule ("tile") and, in the case of the planarity here at stake, its generalization to larger than tetratomics, we explain why carbon [n]triangulenes tend to be planar, while hybrids, where just a few or even all a- or b-type carbon atoms are silicon-substituted (sila-[n]triangulenes), tend to be planar/nonplanar when compared with the unsubstituted carbon-[n]triangulenes. Because other spin states of the parent carbon- and sila-[n]triangulenes tend to correlate with the same tiles, it is conjectured that no structural changes are expected to depend on their spin state. Other polycyclic and sila-compounds are also discussed.
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Affiliation(s)
- A J C Varandas
- School of Physics and Physical Engineering, Qufu Normal University, Qufu 273165, P. R. China
- Department of Physics, Universidade Federal do Espí rito Santo, 29075-910 Vitória, Brazil
- Department of Chemistry and Coimbra Chemistry Centre, University of Coimbra 3004-535 Coimbra, Portugal
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7
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Arasaki Y, Takatsuka K. Energy natural orbital characterization of nonadiabatic electron wavepackets in the densely quasi-degenerate electronic state manifold. J Chem Phys 2023; 158:114102. [PMID: 36948795 DOI: 10.1063/5.0139288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
Abstract
Dynamics and energetic structure of largely fluctuating nonadiabatic electron wavepackets are studied in terms of Energy Natural Orbitals (ENOs) [K. Takatsuka and Y. Arasaki, J. Chem. Phys. 154, 094103 (2021)]. Such huge fluctuating states are sampled from the highly excited states of clusters of 12 boron atoms (B12), which have densely quasi-degenerate electronic excited-state manifold, each adiabatic state of which gets promptly mixed with other states through the frequent and enduring nonadiabatic interactions within the manifold. Yet, the wavepacket states are expected to be of very long lifetimes. This excited-state electronic wavepacket dynamics is extremely interesting but very hard to analyze since they are usually represented in large time-dependent configuration interaction wavefunctions and/or in some other complicated forms. We have found that ENO gives an invariant energy orbital picture to characterize not only the static highly correlated electronic wavefunctions but also those time-dependent electronic wavefunctions. Hence, we first demonstrate how the ENO representation works for some general cases, choosing proton transfer in water dimer and electron-deficient multicenter chemical bonding in diborane in the ground state. We then penetrate with ENO deep into the analysis of the essential nature of nonadiabatic electron wavepacket dynamics in the excited states and show the mechanism of the coexistence of huge electronic fluctuation and rather strong chemical bonds under very random electron flows within the molecule. To quantify the intra-molecular energy flow associated with the huge electronic-state fluctuation, we define and numerically demonstrate what we call the electronic energy flux.
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Affiliation(s)
- Yasuki Arasaki
- Fukui Institute for Fundamental Chemistry, Kyoto University, 606-8103 Kyoto, Japan
| | - Kazuo Takatsuka
- Fukui Institute for Fundamental Chemistry, Kyoto University, 606-8103 Kyoto, Japan
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8
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Galvez Vallejo JL, Tow GM, Maginn EJ, Pham BQ, Datta D, Gordon MS. Quantum Chemical Modeling of Propellant Degradation. J Phys Chem A 2023; 127:1874-1882. [PMID: 36791340 DOI: 10.1021/acs.jpca.2c08722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
An ab initio quantum chemical approach for the modeling of propellant degradation is presented. Using state-of-the-art bonding analysis techniques and composite methods, a series of potential degradation reactions are devised for a sample hydroxyl-terminated-polybutadiene (HTPB) type solid fuel. By applying thermochemical procedures and isodesmic reactions, accurate thermochemical quantities are obtained using a modified G3 composite method based on the resolution of the identity. The calculated heats of formation for the different structures produced presents an ∼2 kcal/mol average error when compared against experimental values.
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Affiliation(s)
- Jorge L Galvez Vallejo
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Garrett M Tow
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Edward J Maginn
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Buu Q Pham
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Dipayan Datta
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
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9
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Tammaro A, Galli DE, Rice JE, Motta M. N-Electron Valence Perturbation Theory with Reference Wave Functions from Quantum Computing: Application to the Relative Stability of Hydroxide Anion and Hydroxyl Radical. J Phys Chem A 2023; 127:817-827. [PMID: 36638358 DOI: 10.1021/acs.jpca.2c07653] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Quantum simulations of the hydroxide anion and hydroxyl radical are reported, employing variational quantum algorithms for near-term quantum devices. The energy of each species is calculated along the dissociation curve, to obtain information about the stability of the molecular species being investigated. It is shown that simulations restricted to valence spaces incorrectly predict the hydroxyl radical to be more stable than the hydroxide anion. Inclusion of dynamical electron correlation from nonvalence orbitals is demonstrated, through the integration of the variational quantum eigensolver and quantum subspace expansion methods in the workflow of N-electron valence perturbation theory, and shown to correctly predict the hydroxide anion to be more stable than the hydroxyl radical, provided that basis sets with diffuse orbitals are also employed. Finally, we calculate the electron affinity of the hydroxyl radical using an aug-cc-pVQZ basis on IBM's quantum devices.
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Affiliation(s)
- Alessandro Tammaro
- Dipartimento di Fisica "Aldo Pontremoli", Università degli Studi di Milano, via Celoria 16, I-20133Milano, Italy
| | - Davide E Galli
- Dipartimento di Fisica "Aldo Pontremoli", Università degli Studi di Milano, via Celoria 16, I-20133Milano, Italy
| | - Julia E Rice
- IBM Quantum, IBM Research Almaden, 650 Harry Road, San Jose, California95120, United States
| | - Mario Motta
- IBM Quantum, IBM Research Almaden, 650 Harry Road, San Jose, California95120, United States
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10
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De J, N S S, Hossain M, Bhattacharjee J. Maximally valent orbitals in systems with non-ideal bond-angles: atomic Wannier orbitals guided by the Mayer bond order. Phys Chem Chem Phys 2023; 25:1717-1727. [PMID: 36562398 DOI: 10.1039/d2cp04259b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
In pursuit of a directed minimal set of basis for systems with non-ideal bond angles, in this work we find the exact orientation of the major overlapping orbitals along the nearest neighbouring coordination segments in a given system such that they maximally represent the covalent interactions throughout the system. We compute Mayer's bond order, akin to Wiberg's bond index, on the basis of atomic Wannier orbitals with customizable non-degenerate hybridization leading to variable orientations, constructed from first principles, in a representative variety of molecules and layered systems. We put such orbitals in perspective with unbiased maximally localized descriptions of bonding and non-bonding orbitals, and energetics to tunneling of electrons through them between nearest neighbours, to describe the different physical aspects of covalent interactions, which are not necessarily represented using a single unique set of atomic or bonding orbitals.
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Affiliation(s)
- Joydev De
- School of Physical Sciences, National Institute of Science Education and Research, A CI of Homi Bhabha National Institute, Odisha-752050, India.
| | - Sujith N S
- School of Physical Sciences, National Institute of Science Education and Research, A CI of Homi Bhabha National Institute, Odisha-752050, India.
| | - Manoar Hossain
- School of Physical Sciences, National Institute of Science Education and Research, A CI of Homi Bhabha National Institute, Odisha-752050, India.
| | - Joydeep Bhattacharjee
- School of Physical Sciences, National Institute of Science Education and Research, A CI of Homi Bhabha National Institute, Odisha-752050, India.
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11
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Leszczyk A, Dome T, Tecmer P, Kedziera D, Boguslawski K. Resolving the π-assisted U-N σ f-bond formation using quantum information theory. Phys Chem Chem Phys 2022; 24:21296-21307. [PMID: 36043327 DOI: 10.1039/d2cp03377a] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We model the potential energy profiles of the UO2 (NCO)Cl2- → NUOCl2- + CO2 reaction pathway [Y. Gong, V. Vallet, M. del Carmen Michelini, D. Rios and J. K. Gibson, J. Phys. Chem. A, 2014, 118, 325-330] using different pair coupled-cluster doubles (pCCD) methods. Specifically, we focus on pCCD and pCCD-tailored coupled cluster models in predicting relative energies for the various intermediates and transition states along the reaction coordinate. Furthermore, we augment our study on energetics with an orbital-pair correlation analysis of the complete reaction pathway that features two distinct paths. Our analysis of orbital correlations sheds new light on the formation and breaking of respective bonds between the uranium, oxygen, and nitrogen atoms along the reaction coordinates where the "yl" bond is broken and a nitrido compound formed. Specifically, the strengthening of the U-N σf-bond is assisted by a π-type interaction that is delocalized over the C-N-U backbone of the UO2 (NCO)Cl2- complex.
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Affiliation(s)
- Aleksandra Leszczyk
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Toruń, Grudziadzka 5, 87-100 Toruń, Poland.
| | - Tibor Dome
- Institute for Theoretical Physics, ETH Zürich, 8093 Zürich, Switzerland.,Institute of Astronomy, University of Cambridge, Madingley Road Cambridge, CB3 0HA, UK
| | - Paweł Tecmer
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Toruń, Grudziadzka 5, 87-100 Toruń, Poland.
| | - Dariusz Kedziera
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100 Toruń, Poland
| | - Katharina Boguslawski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Toruń, Grudziadzka 5, 87-100 Toruń, Poland.
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12
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Mato J, Tzeli D, Xantheas SS. The Many-Body Expansion for Metals I: The Alkaline Earth metals Be, Mg, and Ca. J Chem Phys 2022; 157:084313. [DOI: 10.1063/5.0094598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We examine the Many-Body Expansion (MBE) for alkaline earth metal clusters, Be n, Mg n, Ca n ( n = 4, 5, 6) at the MP2, CCSD(T), MRPT2, and MRCI levels of theory. The magnitude of each term in the MBE is evaluated for several geometrical configurations. We find that the behavior of the MBE for these clusters depends strongly on the geometrical arrangement, and, to a lesser extent, on the level of theory used. Another factor that affects the MBE is the in situ (ground or excited) electronic state of the individual atoms in the cluster. For most geometries, the three-body term is the largest, followed by a steady decrease in absolute energy for subsequent terms. Though these systems exhibit non-negligible multi-reference effects, there was little qualitative difference in the MBE expansion when employing single vs. multi-reference methods. Useful insights into the connectivity and stability of these clusters have been drawn from the respective potential energy surfaces and Quasi-Atomic orbitals for the various dimers, trimers, and tetramers. Through these analyses we investigate the similarities and differences in the binding energies of different size clusters for these metals.
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Affiliation(s)
- Joani Mato
- Chemical Physics, Pacific Northwest National Laboratory, United States of America
| | - Demeter Tzeli
- Department of Chemistry, National and Kapodistrian University of Athens Department of Chemistry, Greece
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13
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Arasaki Y, Takatsuka K. Nature of chemical bond and potential barrier in an invariant energy-orbital picture. J Chem Phys 2022; 156:234102. [PMID: 35732517 DOI: 10.1063/5.0088340] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Physical nature of the chemical bond and potential barrier is studied in terms of energy natural orbitals (ENOs), which are extracted from highly correlated electronic wavefunctions. ENO provides an objective one-electron picture about energy distribution in a molecule, just as the natural orbitals (NOs) represent one electron view about electronic charge distribution. ENO is invariant in the same sense as NO is, that is, ENOs converge to the exact ones as a series of approximate wavefunctions approach the exact one, no matter how the methods of approximation are adopted. Energy distribution analysis based on ENO can give novel insights about the nature of chemical bonding and formation of potential barriers, besides information based on the charge distribution alone. With ENOs extracted from full configuration interaction wavefunctions in a finite yet large enough basis set, we analyze the nature of chemical bonding of three low-lying electronic states of a hydrogen molecule, all being in different classes of the so-called covalent bond. The mechanism of energy lowering in bond formation, which gives a binding energy, is important, yet not the only concern for this small molecule. Another key notion in chemical bonding is whether a potential basin is well generated stiff enough to support a vibrational state(s) on it. Based on the virial theorem in the adiabatic approximation and in terms of the energy and force analyses with ENOs, we study the roles of the electronic kinetic energy and its nuclear derivative(s) on how they determine the curvature (or the force constant) of the potential basins. The same idea is applied to the potential barrier and, thereby, the transition states. The rate constant within the transition-state theory is formally shown to be described in terms of the electronic kinetic energy and the nuclear derivatives only. Thus, the chemical bonding and rate process are interconnected behind the scenes. Besides this aspect, we pay attention to (1) the effects of electron correlation that manifests itself not only in the orbital energy but also in the population of ENOs and (2) the role of nonadiabaticity (diabatic state mixing), resulting in double basins and a barrier on a single potential curve in bond formation. These factors differentiate a covalent bond into subclasses.
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Affiliation(s)
- Yasuki Arasaki
- Fukui Institute for Fundamental Chemistry, Kyoto University, 606-8103 Kyoto, Japan
| | - Kazuo Takatsuka
- Fukui Institute for Fundamental Chemistry, Kyoto University, 606-8103 Kyoto, Japan
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14
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Abstract
According to Ruedenberg's classic treatise on the theory of chemical bonding [K. Ruedenberg, Rev. Mod. Phys. 34, 326-376 (1962)], orbital contraction is an integral consequence of covalent bonding. While the concept is clear, its quantification by quantum chemical calculations is not straightforward, except for the simplest of molecules, such as H2 + and H2. This paper proposes a new, yet simple, approach to the problem, utilizing the modified atomic orbital (MAO) method of Ehrhardt and Ahlrichs [Theor. Chim. Acta 68, 231 (1985)]. Through the use of MAOs, which are an atom-centered minimal basis formed from the molecular and atomic density operators, the wave functions of the species of interest are re-expanded, allowing the computation of the kinetic energy (and any other expectation value) of free and bonded fragments. Thus, it is possible to quantify the intra- and interfragment changes in kinetic energy, i.e., the effects of contraction. Computations are reported for a number of diatomic molecules H2, Li2, B2, C2, N2, O2, F2, CO, P2, and Cl2 and the polyatomics CH3-CH3, CH3-SiH3, CH3-OH, and C2H5-C2H5 (where the single bonds between the heavy atoms are studied) as well as dimers of He, Ne, Ar, and the archetypal ionic molecule NaCl. In all cases, it is found that the formation of a covalent bond is accompanied by an increase in the intra-fragment kinetic energy, an indication of orbital contraction and/or deformation.
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Affiliation(s)
- George B Bacskay
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
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15
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Pancharatna PD, Dar SH, Chowdhury UD, Balakrishnarajan MM. Anatomy of Classical Boron-Boron Bonding: Overlap and sp Dissonance. J Phys Chem A 2022; 126:3219-3228. [PMID: 35579966 DOI: 10.1021/acs.jpca.2c01981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Classical bonding is predominantly understood using the insipid spn hybridization for σ-bonds as well as π bonds and their delocalized variants. Because hybridization ignores intricate differences in the energy and size of valence atomic orbitals, its naïve application to classically bonded boron atoms leads to numerous surprises in bond strengths, frontier MOs/bands, and even geometry. Here we show that the sp dissonance caused by size mismatch between the valence s and p orbitals of boron plays a crucial role in its bonding, subtly distinct from that of carbon and silicon. Unlike the heavier p block elements, boron prefers to actively engage its compact 2s orbitals in bonding. This leads to the overreach of p-p σ-type overlap that reduces its magnitude in the entire B─B bonding range. Consequently, the π-type overlap remains substantial, making its electronic structure visibly distinct in saturated and unsaturated regimes. The deltahedral frameworks offer a compromise by breaking this symmetry-enforced dichotomy of classical σ- and π-type bonding and following alternate electron counts that suit the electron deficiency of the boron. The pathological anatomy of classical B─B σ-bonding also explains the origins of puzzling metallic character and disorder in their classical boride networks even with ideal electron count, unlike deltahedral borides. The implications of sp dissonance are illustrated in classical boron networks of various hybridizations, explaining the unusual preference for unique sp3 lattice with strained four-membered rings in CrB4, origins of observed σ holes in MgB2 that lead to its superconducting nature, and the absence of Peierls distortion in LiB.
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Affiliation(s)
| | - Sohail H Dar
- Department of Chemistry, Pondicherry University, Pondicherry, India 605 014
| | - Unmesh D Chowdhury
- Department of Chemistry, National Institute of Science Education and Research-Bhubaneswar, an OCC of Homi Bhabha National Institute, Odisha, India 752050
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16
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Ruedenberg K. Atoms and interatomic bonding synergism inherent in molecular electronic wave functions. J Chem Phys 2022; 157:024111. [DOI: 10.1063/5.0094609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The chemical model of matter consists of atoms held together by bonds. The success of this model implies that the physical interactions of the electrons and nuclei in molecules combine into compound interactions that create the bonding. In the quantum mechanical description, the modified atoms in molecules and the bonding synergism are contained in the molecular electronic wave function. So far, only part of this information has been recovered from the wave function. Notably, the atoms have remained unidentified in the wave function. One reason is that conventional energy decomposition analyses formulate separate model wave functions, independent of the actual wave function, to represent "prepared atoms" and preconceived interactions, and then intuitively catenate the parts. In the present work, the embedded modified atoms and the inherent physical synergisms between them are determined by a unified derivation entirely from the actual molecular valence space wave function. By means of a series of intrinsic orbital and configurational transformations of the wave function, the energy of formation of a molecule is additively resolved in terms of intra-atomic energy changes, interference energies, quasi-classical, non-classical and charge-transfer Coulombic interactions. The analysis furnishes an algorithm for the quantitative resolution of the energy of formation, which enables analyses elucidating reaction energies.
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Affiliation(s)
- Klaus Ruedenberg
- Department of Chemistry, Iowa State University Department of Chemistry, United States of America
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17
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Osman HHH, Manjón FJ. Metavalent bonding in chalcogenides: DFT-chemical pressure approach. Phys Chem Chem Phys 2022; 24:9936-9942. [PMID: 35437536 DOI: 10.1039/d2cp00954d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding the chemical bond nature has attracted considerable attention as it is crucial to analyze and comprehend the different physical and chemical properties of materials. This work is considered a complementary part of our previous work in studying the nature of different types of bonding interactions in a wide variety of molecules and materials using the DFT Chemical Pressure (CP) approach. Recently, a new type of chemical bond, the metavalent bond (MVB), has been defined. We show how the CP formalism can be used to analyze and study the establishment of MVB in two chalcogenides, GeSe and PbSe, in a similar fashion as the electron localization function (ELF) profiles. This is accomplished by analyzing the CP maps of these two chalcogenides at different pressures (up to 40 GPa for GeSe and 10 GPa for PbSe). The CP maps show distinctive features related to the MVB, providing insights into the existence of such chemical interaction in the crystal structure of the two compounds. Similar to ELF profiles, CP maps can visualize and track the strength of the MVB in GeSe and PbSe under pressure.
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Affiliation(s)
- Hussien Helmy Hassan Osman
- Chemistry Department, Faculty of Science, Helwan University, Ain-Helwan, 11795, Cairo, Egypt. .,Instituto de Diseño para la Fabricación y Producción Automatizada, MALTA Consolider Team, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Francisco Javier Manjón
- Instituto de Diseño para la Fabricación y Producción Automatizada, MALTA Consolider Team, Universitat Politècnica de València, 46022 Valencia, Spain
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18
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Harville T, Gordon MS. Intramolecular Hydrogen Bonding Analysis. J Chem Phys 2022; 156:174302. [DOI: 10.1063/5.0090648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The quasi-atomic orbital (QUAO) bonding analysis is used to study intramolecular hydrogen bonding (IMHB) in salicylic acid and an intermediate that is crucial to the synthesis of aspirin. The bonding analysis rigorously explores IMHB through directly accessing information that is intrinsic to the molecular wave function, thereby bypassing the need for intrinsically biased methods. The variables that effect the strength of IMHB are determined using kinetic bond orders (KBO), QUAO populations, and QUAO hybridizations. Important properties include both the interatomic distance between the hydrogen and oxygen participating in the IMHB and the hybridization on the oxygen. The bonding analysis further shows that each intramolecular hydrogen bond is a 4-electron 3-center bond. The bonding analysis is used to understand how aromatic reactivity changes due to the effect of functional groups on the aromatic ring.
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Affiliation(s)
| | - Mark S. Gordon
- Department of Chemistry, Iowa State University, United States of America
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19
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Varandas AJC. From six to eight Π-electron bare rings of group-XIV elements and beyond: can planarity be deciphered from the "quasi-molecules" they embed? Phys Chem Chem Phys 2022; 24:8488-8507. [PMID: 35343978 DOI: 10.1039/d1cp04130d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ab initio molecular orbital theory is used to study the structures of six and eight π-electron bare rings of group-XIV elements, and even larger [n]annulenes up to C18H18, including some of their mono-, di-, tri-, and tetra-anions. While some of the above rings are planar, others are nonplanar. A much spotlighted case is cyclo-octatetraene (C8H8), which is predicted to be nonplanar together with its heavier group-XIV analogues Si8H8 and Ge8H8, with the solely planar members of its family having the stoichiometric formulas C4Si4H8 and C4Ge4H8. A similar situation arises with the six π-electron bare rings, where benzene and substituted ones up to C3Si3H6 or so are planar, while others are not. However, the explanations encountered in the literature find support in ab initio calculations for such species, often rationalized from distinct calculated features. Using second-order Møller-Plesset perturbation theory and, when affordable (particularly tetratomics, which may allow even higher levels), the coupled-cluster method including single, double, and perturbative triple excitations, a common rationale is suggested based on a novel concept of quasi-molecules or the (3+4)-atom partition scheme. Any criticism of tautology is therefore avoided. The same analysis has also been successfully applied to even larger [n]annulenes, to their mixed family members involving silicon and germanium atoms, and to the C18 carbon ring. Furthermore, it has been extended to annulene anions to check the criteria of the popular Hückel rule for planarity and aromaticity. Exploratory work on cycloarenes is also reported. Besides a partial study of the involved potential energy surfaces, equilibrium geometries and harmonic vibrational frequencies have been calculated anew, for both the parent and the actual prototypes of the quasi-molecules.
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Affiliation(s)
- A J C Varandas
- School of Physics and Physical Engineering, Qufu Normal University, 273165 Qufu, China.,Department of Physics, Universidade Federal do Esp rito Santo, 29075-910 Vitória, Brazil.,Department of Chemistry, and Chemistry Centre, University of Coimbra, 3004-535 Coimbra, Portugal.
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20
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Clement MC, Wang X, Valeev EF. Robust Pipek-Mezey Orbital Localization in Periodic Solids. J Chem Theory Comput 2021; 17:7406-7415. [PMID: 34739235 DOI: 10.1021/acs.jctc.1c00238] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We describe a robust method for determining Pipek-Mezey (PM) Wannier functions (WF), recently introduced by Jónsson et al. (J. Chem. Theor. Chem. 2017, 13, 460), which provide some formal advantages over the more common Boys (also known as maximally-localized) Wannier functions. The Broyden-Fletcher-Goldfarb-Shanno-based PMWF solver is demonstrated to yield dramatically faster convergence compared to the alternatives (steepest ascent and conjugate gradient) in a variety of one-, two-, and three-dimensional solids (including some with vanishing gaps) and can be used to obtain Wannier functions robustly in supercells with thousands of atoms. Evaluation of the PM functional and its gradient in periodic linear combination of atomic orbital representation used a particularly simple definition of atomic charges obtained by Moore-Penrose pseudoinverse projection onto the minimal atomic orbital basis. An automated "canonicalize phase then randomize" method for generating the initial guess for WFs contributes significantly to the robustness of the solver.
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Affiliation(s)
- Marjory C Clement
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Xiao Wang
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States.,Center for Computational Quantum Physics, Flatiron Institute, New York, New York 10010, United States
| | - Edward F Valeev
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
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21
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Galvez Vallejo JL, Heredia JD, Gordon MS. Bonding analysis of water clusters using quasi-atomic orbitals. Phys Chem Chem Phys 2021; 23:18734-18743. [PMID: 34612411 DOI: 10.1039/d1cp02301b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The quasi-atomic orbital (QUAO) bonding analysis introduced by Ruedenberg and co-workers is used to develop an understanding of the hydrogen bonds in small water clusters, from the dimer through the hexamer (bag, boat, book, cyclic, prism and cage conformers). Using kinetic bond orders as a metric, it is demonstrated that as the number of waters in simple cyclic clusters increases, the hydrogen bonds strengthen, from the dimer through the cyclic hexamer. However, for the more complex hexamer isomers, the strength of the hydrogen bonds varies, depending on whether the cluster contains double acceptors and/or double donors. The QUAO analysis also reveals the three-center bonding nature of hydrogen bonds in water clusters.
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22
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Hossain M, De J, Bhattacharjee J. Hybrid Atomic Orbital Basis from First Principles: Bottom-Up Mapping of Self-Energy Correction to Large Covalent Systems. J Phys Chem A 2021; 125:6805-6817. [PMID: 34324816 DOI: 10.1021/acs.jpca.1c00320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Construction of hybrid atomic orbitals is proposed as the approximate common eigenstates of finite first moment matrices. Their hybridization and orientation can be a priori tuned as per their anticipated neighborhood. Their Wannier function counterparts constructed from the Kohn-Sham (KS) single particle states constitute an orthonormal multiorbital tight binding (TB) basis resembling hybrid atomic orbitals locked to their immediate atomic neighborhood, while spanning the subspace of KS states. The proposed basis thus renders predominantly single TB parameters from first principles for each nearest neighbor bond involving no more than two orbitals irrespective of their orientation and also facilitates an easy route for the transfer of such TB parameters across isostructural systems exclusively through mapping of neighborhoods and projection of orbital charge centers. With hybridized 2s, 2p and 3s, 3p valence electrons, the spatial extent of the self-energy correction (SEC) to TB parameters in the proposed basis is found to be localized mostly within the third nearest neighborhood, thus allowing effective transfer of self-energy-corrected TB parameters from smaller reference systems to much larger target systems, with nominal additional computational cost beyond that required for explicit computation of SEC in the reference systems. The proposed approach promises inexpensive estimation of the quasi-particle structures of large covalent systems with workable accuracy.
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Affiliation(s)
- Manoar Hossain
- National Institute of Science Education and Research, Homi Bhaba National Institute, Jatni, Khurda, Bhubaneswar, 752050, Odisha, India
| | - Joydev De
- National Institute of Science Education and Research, Homi Bhaba National Institute, Jatni, Khurda, Bhubaneswar, 752050, Odisha, India
| | - Joydeep Bhattacharjee
- National Institute of Science Education and Research, Homi Bhaba National Institute, Jatni, Khurda, Bhubaneswar, 752050, Odisha, India
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23
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Nascimento MAC. The Valence-Bond (VB) Model and Its Intimate Relationship to the Symmetric or Permutation Group. Molecules 2021; 26:molecules26154524. [PMID: 34361677 PMCID: PMC8347111 DOI: 10.3390/molecules26154524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/06/2021] [Accepted: 07/10/2021] [Indexed: 11/16/2022] Open
Abstract
VB and molecular orbital (MO) models are normally distinguished by the fact the first looks at molecules as a collection of atoms held together by chemical bonds while the latter adopts the view that each molecule should be regarded as an independent entity built up of electrons and nuclei and characterized by its molecular structure. Nevertheless, there is a much more fundamental difference between these two models which is only revealed when the symmetries of the many-electron Hamiltonian are fully taken into account: while the VB and MO wave functions exhibit the point-group symmetry, whenever present in the many-electron Hamiltonian, only VB wave functions exhibit the permutation symmetry, which is always present in the many-electron Hamiltonian. Practically all the conflicts among the practitioners of the two models can be traced down to the lack of permutation symmetry in the MO wave functions. Moreover, when examined from the permutation group perspective, it becomes clear that the concepts introduced by Pauling to deal with molecules can be equally applied to the study of the atomic structure. In other words, as strange as it may sound, VB can be extended to the study of atoms and, therefore, is a much more general model than MO.
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24
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Schoendorff G, Ruedenberg K, Gordon MS. Multiple Bonding in Rhodium Monoboride. Quasi-atomic Analyses of the Ground and Low-Lying Excited States. J Phys Chem A 2021; 125:4836-4846. [PMID: 34042447 DOI: 10.1021/acs.jpca.1c02860] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The bonding structures of the ground state and the lowest five excited states of rhodium monoboride are identified by determining the quasi-atomic orbitals in full valence space MCSCF wave functions and the interactions between these orbitals. A quadruple bond, namely two π-bonds and two σ-bonds, is identified and characterized for the X1Σ+ ground state, in agreement with a previous report (Cheung J. Phys. Chem. Lett. 2020, 11, 659-663). However, in all excited states, the bonding is predicted to be weaker because, in these states, one of the σ-bonding interactions has a small magnitude. In the a3Δ and A1Δ states, the bond order is between a triple and quadruple bond. In the b3Σ+ state, the Rh-B linkage is a triple bond. In the c3Π and B1Π states, the atoms are linked by a double bond due to an additional weakening of the two π-bonds. The decreases in the predicted bond strengths are reflected in the decreases of the predicted binding energies and in the increases of the predicted bond lengths from the X1Σ+ ground state to the c3Π and the B1Π excited states. Notably, the 5pσ orbital of rhodium, which is vacant in the ground state of the atom, plays a significant role in the molecule.
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Affiliation(s)
- George Schoendorff
- Department of Chemistry, Virginia Military Institute, Lexington, Virginia 24450, United States.,Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011-3111, United States
| | - Klaus Ruedenberg
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011-3111, United States
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011-3111, United States
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25
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de Sousa DWO, Nascimento MAC. Substituent Effects on the Quantum Interference of Two-Center One-Electron Bonds: [B 2X 6] - (X = H, F, Cl, CN, OH, CH 3, and OCH 3). J Phys Chem A 2021; 125:4558-4564. [PMID: 34014679 DOI: 10.1021/acs.jpca.1c02771] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The interference energy analysis (IEA) provided by the generalized product function energy partitioning (GPF-EP) method was applied to investigate the influence of the neighboring atoms on the nature of the two-center one-electron (2c1e) bonds in the anion dimers of BX3 species (X = H, F, Cl, CN, OH, CH3, and OCH3). The species were studied at the GVB-PP(6/12).SC(1,2)/6-31**G++ level of calculation. The IEA has revealed that there is a balance between two main factors determining the chemical stability of the species. Quantum interference acts as the sole stabilizing effect in the formation of the chemical bonds, particularly as the result of the drop in kinetic energy, and the electronegativity of the substituent has a direct influence on the magnitude of this effect. The quasi-classical energy is responsible for the destabilizing factors, mainly the group bulkiness, and the "electron-withdrawing" effect in the case of the cyano group.
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26
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Senjean B, Sen S, Repisky M, Knizia G, Visscher L. Generalization of Intrinsic Orbitals to Kramers-Paired Quaternion Spinors, Molecular Fragments, and Valence Virtual Spinors. J Chem Theory Comput 2021; 17:1337-1354. [PMID: 33555866 DOI: 10.1021/acs.jctc.0c00964] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Localization of molecular orbitals finds its importance in the representation of chemical bonding (and antibonding) and in the local correlation treatments beyond mean-field approximation. In this paper, we generalize the intrinsic atomic and bonding orbitals [G. Knizia, J. Chem. Theory Comput. 2013, 9, 11, 4834-4843] to relativistic applications using complex and quaternion spinors, as well as to molecular fragments instead of atomic fragments only. By performing a singular value decomposition, we show how localized valence virtual orbitals can be expressed on this intrinsic minimal basis. We demonstrate our method on systems of increasing complexity, starting from simple cases such as benzene, acrylic acid, and ferrocene molecules, and then demonstrate the use of molecular fragments and inclusion of relativistic effects for complexes containing heavy elements such as tellurium, iridium, and astatine. The aforementioned scheme is implemented into a standalone program interfaced with several different quantum chemistry packages.
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Affiliation(s)
- Bruno Senjean
- Instituut-Lorentz, Universiteit Leiden, P.O. Box 9506, 2300 RA Leiden, The Netherlands
| | - Souloke Sen
- Theoretical Chemistry, Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands
| | - Michal Repisky
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Gerald Knizia
- Department of Chemistry, The Pennsylvania State University, University Park, State College, Pennsylvania 16802, United States
| | - Lucas Visscher
- Theoretical Chemistry, Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands
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27
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Abstract
This work examines the electronic structure and apparent instability of ethylenedione (OCCO), including an analysis of the singlet and triplet potential energy surfaces along the bending vibrations. While the singlet state is inherently unstable due to the Renner-Teller effect, theory predicts the triplet state to have a stable minimum on the potential energy surface. The stability of the triplet state is examined in detail, taking into account spin-orbit interactions. Using multireference quantum chemical methods, the lifetime of the triplet state is estimated to be in the picosecond range, significantly lower than previously computed. A quasi-atomic molecular orbital (QUAO) analysis is also used to elucidate the nature of bonding along the potential energy surface in both the singlet and triplet states. These calculations confirm the transient nature of the OCCO molecule, although they do not fully explain the lack of experimental detection via spectroscopy, which is known have the capability to probe even shorter lifetimes.
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Affiliation(s)
- Joani Mato
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - David Poole
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
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28
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Guidez EB, Gordon MS, Ruedenberg K. Why is Si 2H 2 Not Linear? An Intrinsic Quasi-Atomic Bonding Analysis. J Am Chem Soc 2020; 142:13729-13742. [PMID: 32662651 DOI: 10.1021/jacs.0c03082] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The molecular energy of Si2H2 geometric structures increases in the order dibridged < trans-bent < linear, in contrast to acetylene, C2H2, for which the linear structure is the global minimum. In this study, the intra-atomic (antibonding) and bonding contributions to the total molecular energy of these valence isoelectronic molecules are computed by expressing the density matrices of the full valence space multiconfiguration self-consistent field wave function in terms of quasi-atomic orbitals. The analysis shows that the intra-atomic contributions to the molecular energy become less favorable in the order dibridged → trans-bent → linear for both C2H2 and Si2H2. By contrast, the inter-atomic bonding contributions become energetically more favorable in that order for both C2H2 and Si2H2. The two systems differ as follows. For Si2H2, the antibonding intra-atomic energy changes that occur when the dibridged molecule reconstructs into the trans-bent and linear structures prevail over the interatomic interactions that induce bond formation. In contrast, for C2H2, the interatomic interactions that create bonds prevail over the intra-atomic energy changes that occur when the dibridged molecule reconstructs into the trans-bent and linear structures. The intra-atomic energy changes that occur in these systems are related to the hybridization of the heavy atoms in an analogous manner to the hybridization of C in CH4 from (2s)2(2p)2 to sp3 hybrid orbitals.
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Affiliation(s)
- Emilie B Guidez
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80204, United States
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory USDOE, Iowa State University, Ames, Iowa 50011, United States
| | - Klaus Ruedenberg
- Department of Chemistry and Ames Laboratory USDOE, Iowa State University, Ames, Iowa 50011, United States
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29
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Barca GMJ, Bertoni C, Carrington L, Datta D, De Silva N, Deustua JE, Fedorov DG, Gour JR, Gunina AO, Guidez E, Harville T, Irle S, Ivanic J, Kowalski K, Leang SS, Li H, Li W, Lutz JJ, Magoulas I, Mato J, Mironov V, Nakata H, Pham BQ, Piecuch P, Poole D, Pruitt SR, Rendell AP, Roskop LB, Ruedenberg K, Sattasathuchana T, Schmidt MW, Shen J, Slipchenko L, Sosonkina M, Sundriyal V, Tiwari A, Galvez Vallejo JL, Westheimer B, Włoch M, Xu P, Zahariev F, Gordon MS. Recent developments in the general atomic and molecular electronic structure system. J Chem Phys 2020; 152:154102. [PMID: 32321259 DOI: 10.1063/5.0005188] [Citation(s) in RCA: 506] [Impact Index Per Article: 126.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A discussion of many of the recently implemented features of GAMESS (General Atomic and Molecular Electronic Structure System) and LibCChem (the C++ CPU/GPU library associated with GAMESS) is presented. These features include fragmentation methods such as the fragment molecular orbital, effective fragment potential and effective fragment molecular orbital methods, hybrid MPI/OpenMP approaches to Hartree-Fock, and resolution of the identity second order perturbation theory. Many new coupled cluster theory methods have been implemented in GAMESS, as have multiple levels of density functional/tight binding theory. The role of accelerators, especially graphical processing units, is discussed in the context of the new features of LibCChem, as it is the associated problem of power consumption as the power of computers increases dramatically. The process by which a complex program suite such as GAMESS is maintained and developed is considered. Future developments are briefly summarized.
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Affiliation(s)
- Giuseppe M J Barca
- Research School of Computer Science, Australian National University, Canberra, ACT 2601, Australia
| | - Colleen Bertoni
- Argonne Leadership Computing Facility, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Laura Carrington
- EP Analytics, 12121 Scripps Summit Dr. Ste. 130, San Diego, California 92131, USA
| | - Dipayan Datta
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Nuwan De Silva
- Department of Physical and Biological Sciences, Western New England University, Springfield, Massachusetts 01119, USA
| | - J Emiliano Deustua
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Umezono 1-1-1, Tsukuba 305-8568, Japan
| | - Jeffrey R Gour
- Microsoft, 15590 NE 31st St., Redmond, Washington 98052, USA
| | - Anastasia O Gunina
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Emilie Guidez
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217, USA
| | - Taylor Harville
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Stephan Irle
- Computational Science and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - Joe Ivanic
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - Karol Kowalski
- Physical Sciences Division, Battelle, Pacific Northwest National Laboratory, K8-91, P.O. Box 999, Richland, Washington 99352, USA
| | - Sarom S Leang
- EP Analytics, 12121 Scripps Summit Dr. Ste. 130, San Diego, California 92131, USA
| | - Hui Li
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588, USA
| | - Wei Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, People's Republic of China
| | - Jesse J Lutz
- Center for Computing Research, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - Ilias Magoulas
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Joani Mato
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Vladimir Mironov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow 119991, Russian Federation
| | - Hiroya Nakata
- Kyocera Corporation, Research Institute for Advanced Materials and Devices, 3-5-3 Hikaridai Seika-cho, Souraku-gun, Kyoto 619-0237, Japan
| | - Buu Q Pham
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Piotr Piecuch
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - David Poole
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Spencer R Pruitt
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Alistair P Rendell
- Research School of Computer Science, Australian National University, Canberra, ACT 2601, Australia
| | - Luke B Roskop
- Cray Inc., a Hewlett Packard Enterprise Company, 2131 Lindau Ln #1000, Bloomington, Minnesota 55425, USA
| | - Klaus Ruedenberg
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | | | - Michael W Schmidt
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Jun Shen
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Lyudmila Slipchenko
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Masha Sosonkina
- Department of Computational Modeling and Simulation Engineering, Old Dominion University, Norfolk, Virginia 23529, USA
| | - Vaibhav Sundriyal
- Department of Computational Modeling and Simulation Engineering, Old Dominion University, Norfolk, Virginia 23529, USA
| | - Ananta Tiwari
- EP Analytics, 12121 Scripps Summit Dr. Ste. 130, San Diego, California 92131, USA
| | - Jorge L Galvez Vallejo
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Bryce Westheimer
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Marta Włoch
- 530 Charlesina Dr., Rochester, Michigan 48306, USA
| | - Peng Xu
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Federico Zahariev
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
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30
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Reuter L, Lüchow A. On the connection between probability density analysis, QTAIM, and VB theory. Phys Chem Chem Phys 2020; 22:25892-25903. [PMID: 33159782 DOI: 10.1039/d0cp02209h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Classification of bonds is essential for understanding and predicting the reactivity of chemical compounds. This classification mainly manifests in the bond order and the contribution of different Lewis resonance structures. Here, we outline a first principles approach to obtain these orders and contributions for arbitrary wave functions in a manner that is both, related to the quantum theory of atoms in molecules and consistent with valence bond theory insight: the Lewis structures arise naturally as attractors of the all-electron probability density |Ψ|2. Doing so, we introduce a valence bond weight definition that does not collapse in the basis set limit.
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Affiliation(s)
- Leonard Reuter
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52074 Aachen, Germany.
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31
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Schoendorff G, Schmidt MW, Ruedenberg K, Gordon MS. Quasi-Atomic Bond Analyses in the Sixth Period: II. Bond Analyses of Cerium Oxides. J Phys Chem A 2019; 123:5249-5256. [PMID: 31199636 DOI: 10.1021/acs.jpca.9b04024] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The role of the 4f orbitals in bonding is examined for the molecules cerium monoxide and cerium dioxide that have cerium formally in the +2 and +4 oxidation states, respectively. It is shown that the 4f orbitals are used primarily for polarization of the 5d orbitals when cerium is in the lower oxidation state, while the 4f orbitals play a significant role in chemical bonding via 5d/4f hybridization when cerium is in the +4 oxidation state.
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Affiliation(s)
- George Schoendorff
- Mund-Lagowski Department of Chemistry and Biochemistry , Bradley University , Peoria , Illinois 61625 , United States
| | - Michael W Schmidt
- Department of Chemistry , Iowa State University , Ames , Iowa 50011-3111 , United States
| | - Klaus Ruedenberg
- Department of Chemistry , Iowa State University , Ames , Iowa 50011-3111 , United States
| | - Mark S Gordon
- Department of Chemistry , Iowa State University , Ames , Iowa 50011-3111 , United States
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32
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Schoendorff G, West AC, Schmidt MW, Ruedenberg K, Gordon MS. Quasi-Atomic Bond Analyses in the Sixth Period: I. Relativistic Accurate Atomic Minimal Basis Sets for the Elements Cesium to Radon. J Phys Chem A 2019; 123:5242-5248. [DOI: 10.1021/acs.jpca.9b04023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- George Schoendorff
- Mund-Lagowski Department of Chemistry and Biochemistry, Bradley University, Peoria, Illinois 61625, United States
| | - Aaron C. West
- Department of Chemistry and Ames Laboratory USDOE, Iowa State University, Ames, Iowa 50011-3111, United States
| | - Michael W. Schmidt
- Department of Chemistry and Ames Laboratory USDOE, Iowa State University, Ames, Iowa 50011-3111, United States
| | - Klaus Ruedenberg
- Department of Chemistry and Ames Laboratory USDOE, Iowa State University, Ames, Iowa 50011-3111, United States
| | - Mark S. Gordon
- Department of Chemistry and Ames Laboratory USDOE, Iowa State University, Ames, Iowa 50011-3111, United States
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33
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Krause C, Werner HJ. Scalable Electron Correlation Methods. 6. Local Spin-Restricted Open-Shell Second-Order Møller-Plesset Perturbation Theory Using Pair Natural Orbitals: PNO-RMP2. J Chem Theory Comput 2019; 15:987-1005. [PMID: 30571916 DOI: 10.1021/acs.jctc.8b01012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a (near) linear scaling implementation of high-spin open-shell Møller-Plesset perturbation theory using pair natural orbitals (PNO-RMP2). The theory is based on a new variant of open-shell MP2 which is fully spin-adapted and uses a single set of spin-free amplitudes, as in closed-shell MP2. This method, denoted SROMP2, is invariant to unitary orbital transformations within the closed, open, and virtual orbital subspaces. Accordingly, only a single set of PNOs per spatial orbital pair is needed, and the efficiency is similar to closed-shell calculations. The PNOs are obtained using a semicanonical approximation with large domains of projected atomic orbitals (PAOs). Linear scaling is achieved provided that the open-shell orbitals are local, and distant pairs are treated by multipole approximations. The method is efficiently parallelized. The convergence of ionization and reaction energies as a function of the PAO and PNO domain sizes is demonstrated and found to be very similar as for closed-shell calculations. The suitability of the PNOs for explicitly correlated PNO-RCCSD-F12 calculations is also tested. So far, this method is only simulated using a conventional program with appropriate projections to the PAO and PNO subspaces. It is demonstrated for radical stabilization energies as well as ionization potentials that the errors caused by the local domain approximations with our default thresholds are negligible.
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Affiliation(s)
- Christine Krause
- Institut für Theoretische Chemie , Universität Stuttgart , Pfaffenwaldring 55 , D-70569 Stuttgart , Germany
| | - Hans-Joachim Werner
- Institut für Theoretische Chemie , Universität Stuttgart , Pfaffenwaldring 55 , D-70569 Stuttgart , Germany
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34
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Duchimaza Heredia JJ, Sadow AD, Gordon MS. A Quasi-Atomic Analysis of Three-Center Two-Electron Zr-H-Si Interactions. J Phys Chem A 2018; 122:9653-9669. [PMID: 30481021 DOI: 10.1021/acs.jpca.8b09530] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A comprehensive analysis of the bonding structure of the disilyl zirconocene amide cation {Cp2Zr[N(SiHMe2)2]}+ is conducted by application of an intrinsic orbital localization method that yields quasi-atomic orbitals (QUAOs). An emphasis is placed on describing a previously characterized three-center two-electron interaction between zirconium, hydrogen, and silicon that presents structural and spectroscopic features similar to that of agostic bonds. Expressions of the first-order density matrix in terms of the QUAOs yields bond orders (BOs), kinetic bond orders (KBOs), and the extent of transfer of charge that are useful to determine the electronic nature of the Zr-H-Si bond. The interactions between the QUAOs demonstrate the importance of vicinal interactions in the stabilization of the molecule. In addition, the evolution of the QUAOs during reactions with Lewis bases reveals the role of the Zr-H-Si interaction in facilitating the reaction.
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Affiliation(s)
| | - Aaron D Sadow
- Department of Chemistry Iowa State University , Ames , Iowa 50014 , United States
| | - Mark S Gordon
- Department of Chemistry Iowa State University , Ames , Iowa 50014 , United States
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35
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Dornbach M, Werner HJ. Analytical energy gradients for local second-order Møller-Plesset perturbation theory using intrinsic bond orbitals. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1537529] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Mark Dornbach
- Institut für Theoretische Chemie, Universität Stuttgart, Stuttgart, Germany
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36
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37
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Conrad JA, Pruitt SR, Gordon MS. Proton Transfer in 1,2,4-Triazolium Dinitramide: Effect of Aqueous Microsolvation. J Phys Chem A 2018; 122:7443-7454. [PMID: 30129759 DOI: 10.1021/acs.jpca.8b06348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The gas phase proton transfer process in 1,2,4-triazolium dinitramide (TD) was studied using second-order perturbation theory to determine how the presence of one and two water molecules modifies the potential energy surface that connects the ion pair to the neutral pair. The presence of one water molecule can introduce small proton transfer energy barriers that separate the ion pair from the lower-energy neutral pair. These energy barriers are easily surmounted. Reaction paths were determined for single proton transfers and double proton transfers via one water molecule. In the presence of two water molecules, the global minimum is an ion pair, as are most of the lower-energy local minima. Energy barriers for single, double, and triple proton transfers were also found for TD in the presence of two water molecules. One TD ion pair structure with two water molecules has no corresponding neutral pair energy minimum. A quasi-atomic orbital analysis is used to understand the nature of the bonding in the various species studied in this work.
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Affiliation(s)
- Justin A Conrad
- Department of Chemistry , Iowa State University , Ames , Iowa 50011 , United States
| | - Spencer R Pruitt
- Academic & Research Computing , Worcester Polytechnic Institute , Worcester , Massachusetts 01609 , United States
| | - Mark S Gordon
- Department of Chemistry , Iowa State University , Ames , Iowa 50011 , United States
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38
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Maximal orbital analysis of molecular wavefunctions. J Comput Chem 2018; 40:39-50. [DOI: 10.1002/jcc.25385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 06/04/2018] [Accepted: 06/05/2018] [Indexed: 11/07/2022]
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39
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Ma Q, Werner H. Explicitly correlated local coupled‐cluster methods using pair natural orbitals. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1371] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Qianli Ma
- Institute for Theoretical ChemistryUniversity of StuttgartStuttgartGermany
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40
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Ivanic J, Schmidt MW. Hybrid Correlation Energy (HyCE): An Approach Based on Separate Evaluations of Internal and External Components. J Phys Chem A 2018; 122:5223-5237. [DOI: 10.1021/acs.jpca.8b01794] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joseph Ivanic
- Advanced Biomedical Computational Sciences Group, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland 21702, United States
| | - Michael W. Schmidt
- Department of Chemistry and Ames Laboratory (US-DOE), Iowa State University, Ames, Iowa 50011, United States
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41
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Duchimaza Heredia JJ, Ruedenberg K, Gordon MS. Quasi-Atomic Bonding Analysis of Xe-Containing Compounds. J Phys Chem A 2018. [DOI: 10.1021/acs.jpca.8b00115] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Klaus Ruedenberg
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Mark S. Gordon
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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42
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Osman HH, Salvadó MA, Pertierra P, Engelkemier J, Fredrickson DC, Recio JM. Chemical Pressure Maps of Molecules and Materials: Merging the Visual and Physical in Bonding Analysis. J Chem Theory Comput 2018; 14:104-114. [PMID: 29211959 DOI: 10.1021/acs.jctc.7b00943] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The characterization of bonding interactions in molecules and materials is one of the major applications of quantum mechanical calculations. Numerous schemes have been devised to identify and visualize chemical bonds, including the electron localization function, quantum theory of atoms in molecules, and natural bond orbital analysis, whereas the energetics of bond formation are generally analyzed in qualitative terms through various forms of energy partitioning schemes. In this Article, we illustrate how the chemical pressure (CP) approach recently developed for analyzing atomic size effects in solid state compounds provides a basis for merging these two approaches, in which bonds are revealed through the forces of attraction and repulsion acting between the atoms. Using a series of model systems that include simple molecules (H2, CO2, and S8), extended structures (graphene and diamond), and systems exhibiting intermolecular interactions (ice and graphite), as well as simple representatives of metallic and ionic bonding (Na and NaH, respectively), we show how CP maps can differentiate a range of bonding phenomena. The approach also allows for the partitioning of the potential and kinetic contributions to the interatomic interactions, yielding schemes that capture the physical model for the chemical bond offered by Ruedenberg and co-workers.
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Affiliation(s)
- Hussien H Osman
- MALTA-Consolider Team and Departamento de Química Física y Analítica, Universidad de Oviedo , E-33006 Oviedo, Spain.,Department of Chemistry, Faculty of Science, Helwan University , Ain-Helwan, 11795 Cairo, Egypt
| | - Miguel A Salvadó
- MALTA-Consolider Team and Departamento de Química Física y Analítica, Universidad de Oviedo , E-33006 Oviedo, Spain
| | - Pilar Pertierra
- MALTA-Consolider Team and Departamento de Química Física y Analítica, Universidad de Oviedo , E-33006 Oviedo, Spain
| | - Joshua Engelkemier
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Daniel C Fredrickson
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - J Manuel Recio
- MALTA-Consolider Team and Departamento de Química Física y Analítica, Universidad de Oviedo , E-33006 Oviedo, Spain.,Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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43
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Derricotte WD, Evangelista FA. Localized Intrinsic Valence Virtual Orbitals as a Tool for the Automatic Classification of Core Excited States. J Chem Theory Comput 2017; 13:5984-5999. [DOI: 10.1021/acs.jctc.7b00493] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Wallace D. Derricotte
- Department of Chemistry and Cherry
L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Francesco A. Evangelista
- Department of Chemistry and Cherry
L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
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44
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Abstract
This work addresses the continuing disagreement between two schools of thought concerning the mechanism of covalent bonding. According to Hellmann, Ruedenberg, and Kutzelnigg, covalent bonding is a quantum mechanical phenomenon whereby lowering of the kinetic energy associated with electron sharing, i.e., delocalization, is the key stabilization mechanism. The opposing view of Slater, Feynman, and Bader has maintained that the source of stabilization is electrostatic potential energy lowering due to electron density redistribution to binding regions between nuclei. Following our study of H2+ we present an analogous detailed study of H2 where bonding involves an electron pair with repulsion and correlation playing a significant role in its properties. We use a range of different computational approaches to study and reveal the relevant contributions to bonding as seen in the electron density and corresponding kinetic and potential energy distributions. The energetics associated with the more complex electronic structure of H2, when examined in detail, clearly agrees with the analysis of Ruedenberg; i.e., covalent bonding is due to a decrease in the interatomic kinetic energy resulting from electronic delocalization. Our results support the view that covalent bonding is a quantum dynamical phenomenon requiring a properly quantized kinetic energy to be used in its description.
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Affiliation(s)
- George B Bacskay
- School of Chemistry, The University of Sydney , Sydney, NSW 2006, Australia
| | - Sture Nordholm
- Department of Chemistry and Molecular Biology, The University of Gothenburg , SE-412 96 Göteborg, Sweden
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45
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Heidar-Zadeh F, Ayers PW, Verstraelen T, Vinogradov I, Vöhringer-Martinez E, Bultinck P. Information-Theoretic Approaches to Atoms-in-Molecules: Hirshfeld Family of Partitioning Schemes. J Phys Chem A 2017; 122:4219-4245. [DOI: 10.1021/acs.jpca.7b08966] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Farnaz Heidar-Zadeh
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
- Center for Molecular Modeling, Ghent University, Technologiepark 903, 9052 Zwijnaarde, Belgium
- Department of Chemistry, Ghent University, Krijgslaan 281 (S3), 9000 Gent, Belgium
| | - Paul W. Ayers
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Toon Verstraelen
- Center for Molecular Modeling, Ghent University, Technologiepark 903, 9052 Zwijnaarde, Belgium
| | - Ivan Vinogradov
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Esteban Vöhringer-Martinez
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile
| | - Patrick Bultinck
- Department of Chemistry, Ghent University, Krijgslaan 281 (S3), 9000 Gent, Belgium
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46
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West AC. Atom-Based Strong Correlation Method: An Orbital Selection Algorithm. J Phys Chem A 2017; 121:8912-8926. [DOI: 10.1021/acs.jpca.7b08482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Aaron C. West
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
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47
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West AC, Duchimaza-Heredia JJ, Gordon MS, Ruedenberg K. Identification and Characterization of Molecular Bonding Structures by ab initio Quasi-Atomic Orbital Analyses. J Phys Chem A 2017; 121:8884-8898. [PMID: 29135255 DOI: 10.1021/acs.jpca.7b07054] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The quasi-atomic analysis of ab initio electronic wave functions in full valence spaces, which was developed in preceding papers, yields oriented quasi-atomic orbitals in terms of which the ab initio molecular wave function and energy can be expressed. These oriented quasi-atomic orbitals are the rigorous ab initio counterparts to the conceptual bond forming atomic hybrid orbitals of qualitative chemical reasoning. In the present work, the quasi-atomic orbitals are identified as bonding orbitals, lone pair orbitals, radical orbitals, vacant orbitals and orbitals with intermediate character. A program determines the bonding characteristics of all quasi-atomic orbitals in a molecule on the basis of their occupations, bond orders, kinetic bond orders, hybridizations and local symmetries. These data are collected in a record and provide the information for a comprehensive understanding of the synergism that generates the bonding structure that holds the molecule together. Applications to a series of molecules exhibit the complete bonding structures that are embedded in their ab initio wave functions. For the strong bonds in a molecule, the quasi-atomic orbitals provide quantitative ab initio amplifications of the Lewis dot symbols. Beyond characterizing strong bonds, the quasi-atomic analysis also yields an understanding of the weak interactions, such as vicinal, hyperconjugative and radical stabilizations, which can make substantial contributions to the molecular bonding structure.
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Affiliation(s)
- Aaron C West
- Department of Chemistry and Ames Laboratory USDOE Iowa State University , Ames, Iowa 50011, United States
| | - Juan J Duchimaza-Heredia
- Department of Chemistry and Ames Laboratory USDOE Iowa State University , Ames, Iowa 50011, United States
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory USDOE Iowa State University , Ames, Iowa 50011, United States
| | - Klaus Ruedenberg
- Department of Chemistry and Ames Laboratory USDOE Iowa State University , Ames, Iowa 50011, United States
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48
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Sousa DWOD, Nascimento MAC. Are One-Electron Bonds Any Different from Standard Two-Electron Covalent Bonds? Acc Chem Res 2017; 50:2264-2272. [PMID: 28786664 DOI: 10.1021/acs.accounts.7b00260] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The nature of the chemical bond is perhaps the central subject in theoretical chemistry. Our understanding of the behavior of molecules developed amazingly in the last century, mostly with the rise of quantum mechanics (QM) and QM-based theories such as valence bond theory and molecular orbital theory. Such theories are very successful in describing molecular properties, but they are not able to explain the origin of the chemical bond. This problem was first analyzed in the 1960s by Ruedenberg, who showed that covalent bonds are the direct result of quantum interference between one-electron states. The generality of this result and its quantification were made possible through the recent development of the generalized product function energy partitioning (GPF-EP) method by our group, which allows the partitioning of the electronic density and energy into their interference and quasi-classical (noninterference) contributions. Furthermore, with GPF wave functions these effects can be analyzed separately for each bond of a molecule. This interference energy analysis has been applied to a large variety of molecules, including diatomics and polyatomics, molecules with single, double, and triple bonds, molecules with different degrees of polarity, linear or branched molecules, cyclic or acyclic molecules, conjugated molecules, and aromatics, in order to verify the role played by quantum interference. In all cases the conclusion is exactly the same: for each bond in each of the molecules considered, the main contribution to its stability comes from the interference term. Two-center one-electron (2c1e) bonds are the simplest kind of chemical bonds. Yet they are often viewed as odd or unconventional cases of bonding. Are they any different from conventional (2c2e) bonds? If so, what differences can we expect in the nature of (2c1e) bonds relative to electron-pair bonds? In this Account, we extend the GPF-EP method to describe bonds involving N electrons in M orbitals (N < M) and show its application to (2c1e) bonds. As examples we chose the molecules H2+, H3C·CH3+, B2H4-, [Cu·BH3(PH3)3], and an alkali-metal cation dimer, and we evaluated the components of the electronic energy and density, which account for the formation of the bond, and compared the results with those for the respective analogous molecules exhibiting the "conventional" two-electron bond. In all cases, it was verified that interference is the dominant effect for the one-electron bonds. The GPF-EP results clearly indicate that molecules exhibiting (2c1e) bonds should not be considered as special systems, since one- and two-electron bonds result from quantum interference and therefore there is no conceptual difference between them. Moreover, these results show that quantum interference provides a way to unify the chemical bond concept.
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Affiliation(s)
- David Wilian Oliveira de Sousa
- Instituto de Química, Universidade Federal do Rio de Janeiro Cidade Universitária, CT Bloco
A Sala 412, 21941-909 Rio de Janeiro-RJ, Brazil
| | - Marco Antonio Chaer Nascimento
- Instituto de Química, Universidade Federal do Rio de Janeiro Cidade Universitária, CT Bloco
A Sala 412, 21941-909 Rio de Janeiro-RJ, Brazil
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49
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Sayfutyarova ER, Sun Q, Chan GKL, Knizia G. Automated Construction of Molecular Active Spaces from Atomic Valence Orbitals. J Chem Theory Comput 2017; 13:4063-4078. [DOI: 10.1021/acs.jctc.7b00128] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Elvira R. Sayfutyarova
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08540, United States
- Division
of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Qiming Sun
- Division
of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Garnet Kin-Lic Chan
- Division
of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Gerald Knizia
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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50
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Lefebvre C, Rubez G, Khartabil H, Boisson JC, Contreras-García J, Hénon E. Accurately extracting the signature of intermolecular interactions present in the NCI plot of the reduced density gradient versus electron density. Phys Chem Chem Phys 2017; 19:17928-17936. [PMID: 28664951 DOI: 10.1039/c7cp02110k] [Citation(s) in RCA: 691] [Impact Index Per Article: 98.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
An electron density (ED)-based methodology is developed for the automatic identification of intermolecular interactions using pro-molecular density. The expression of the ED gradient in terms of atomic components furnishes the basis for the Independent Gradient Model (IGM). This model leads to a density reference for non interacting atoms/fragments where the atomic densities are added whilst their interaction turns off. Founded on this ED reference function that features an exponential decay also in interference regions, IGM model provides a way to identify and quantify the net ED gradient attenuation due to interactions. Using an intra/inter uncoupling scheme, a descriptor (δginter) is then derived that uniquely defines intermolecular interaction regions. An attractive feature of the IGM methodology is to provide a workflow that automatically generates data composed solely of intermolecular interactions for drawing the corresponding 3D isosurface representations.
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Affiliation(s)
- Corentin Lefebvre
- Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, University of Reims Champagne-Ardenne, BP 1039, 51687 Reims, France.
| | - Gaëtan Rubez
- Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, University of Reims Champagne-Ardenne, BP 1039, 51687 Reims, France. and CReSTIC EA 3804, University of Reims Champagne-Ardenne, 51687 Reims, France and ATOS Company, 1 rue de Provence, 38130 Echirolles, France
| | - Hassan Khartabil
- Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, University of Reims Champagne-Ardenne, BP 1039, 51687 Reims, France. and Campus Universitaire des Ardennes, 4 bd Jean Delautre, 08000 Charleville-Mézières, France
| | | | - Julia Contreras-García
- Sorbonne Universités, UPMC Univ Paris 06, UMR CNRS 7616, Laboratoire de Chimie Théorique, Paris, France and CNRS, UMR 7616, Laboratoire de Chimie Théorique, Paris, France
| | - Eric Hénon
- Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, University of Reims Champagne-Ardenne, BP 1039, 51687 Reims, France.
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