1
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Mishra A, Kim J, Kim SK, Willitsch S. Isomeric and rotational effects in the chemi-ionisation of 1,2-dibromoethene with metastable neon atoms. Faraday Discuss 2024. [PMID: 38805255 DOI: 10.1039/d3fd00172e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The specific geometry of a molecule can have a pronounced influence on its chemical reactivity. However, experimental data on reactions of individual molecular isomers are still sparse because they are often difficult to separate and frequently interconvert into one another under ambient conditions. Here, we employ a novel crossed-beam experiment featuring an electrostatically controlled molecular beam combined with a source for radicals and metastables to spatially separate the cis and trans stereoisomers as well as individual rotational states of 1,2-dibromoethene and study their specific reactivities in the chemi-ionisation reaction with excited neon atoms. The experiments reveal pronounced isomeric and rotational specificities in the rates and product branching ratios of the reaction. The present study underlines the importance and combined role of molecular geometry and of rotational motion in the dynamics of chemi-ionisation reactions.
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Affiliation(s)
- Amit Mishra
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056, Basel, Switzerland.
| | - Junggil Kim
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea.
| | - Sang Kyu Kim
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea.
| | - Stefan Willitsch
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056, Basel, Switzerland.
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2
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Sherard MM, Kaplan JS, Simpson JH, Kittredge KW, Leopold MC. Functionalized Gold Nanoparticles and Halogen Bonding Interactions Involving Fentanyl and Fentanyl Derivatives. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:917. [PMID: 38869542 PMCID: PMC11173406 DOI: 10.3390/nano14110917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/14/2024] [Accepted: 05/19/2024] [Indexed: 06/14/2024]
Abstract
Fentanyl (FTN) and synthetic analogs of FTN continue to ravage populations across the globe, including in the United States where opioids are increasingly being used and abused and are causing a staggering and growing number of overdose deaths each year. This growing pandemic is worsened by the ease with which FTN can be derivatized into numerous derivatives. Understanding the chemical properties/behaviors of the FTN class of compounds is critical for developing effective chemical detection schemes using nanoparticles (NPs) to optimize important chemical interactions. Halogen bonding (XB) is an intermolecular interaction between a polarized halogen atom on a molecule and e--rich sites on another molecule, the latter of which is present at two or more sites on most fentanyl-type structures. Density functional theory (DFT) is used to identify these XB acceptor sites on different FTN derivatives. The high toxicity of these compounds necessitated a "fragmentation" strategy where smaller, non-toxic molecules resembling parts of the opioids acted as mimics of XB acceptor sites present on intact FTN and its derivatives. DFT of the fragments' interactions informed solution measurements of XB using 19F NMR titrations as well as electrochemical measurements of XB at self-assembled monolayer (SAM)-modified electrodes featuring XB donor ligands. Gold NPs, known as monolayer-protected clusters (MPCs), were also functionalized with strong XB donor ligands and assembled into films, and their interactions with FTN "fragments" were studied using voltammetry. Ultimately, spectroscopy and TEM analysis were combined to study whole-molecule FTN interactions with the functionalized MPCs in solution. The results suggested that the strongest XB interaction site on FTN, while common to most of the drug's derivatives, is not strong enough to induce NP-aggregation detection but may be better exploited in sensing schemes involving films.
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Affiliation(s)
- Molly M. Sherard
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, VA 23173, USA; (M.M.S.); (J.S.K.); (J.H.S.)
| | - Jamie S. Kaplan
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, VA 23173, USA; (M.M.S.); (J.S.K.); (J.H.S.)
| | - Jeffrey H. Simpson
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, VA 23173, USA; (M.M.S.); (J.S.K.); (J.H.S.)
| | - Kevin W. Kittredge
- Department of Chemistry, Joan P. Brock School of Math and Natural Sciences, Virginia Wesleyan College, Virginia Beach, VA 23455, USA;
| | - Michael C. Leopold
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, VA 23173, USA; (M.M.S.); (J.S.K.); (J.H.S.)
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3
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Pomogaeva AV, Lisovenko AS, Timoshkin AY. Structures and stability of I 2 and ICl complexes with pyridine: Ab initio and DFT study. J Comput Chem 2024; 45:903-914. [PMID: 38165152 DOI: 10.1002/jcc.27300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/30/2023] [Accepted: 12/02/2023] [Indexed: 01/03/2024]
Abstract
Theoretical investigation of thermodynamic stability and bonding features of possible isomers of the molecular and ionic complexes of pyridine with molecular iodine and iodine monochloride IX (X = I,Cl) is presented. M06-2X DFT functional is found to provide bond distances and dissociation energies which are close to those obtained at high-level ab initio CCSD(T)/aug-cc-pvtz//CCSD/aug-cc-pvtz benchmark computations for the most stable isomers, formed via donation of a lone pair of nitrogen atom of pyridine to the iodine atom. These isomers are by 23-33 kJ mol-1 (in case of I2) and by 39-56 kJ mol-1 (in case of ICl) more stable than other molecular complexes. T-shaped π-σ* bonded isomers turn out to be energetically comparable with van der Waals bound compounds. Among the ionic isomers, structures featuring [IPy2]+ cation with I3 - or ICl2 - counterions are more stable. Oligomerization favors ionic isomers starting from the tetrameric clusters of the composition (IX)4Py4.
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Affiliation(s)
- Anna V Pomogaeva
- Institute of Chemistry, Saint Petersburg State University, St. Petersburg, Russia
| | - Anna S Lisovenko
- Institute of Chemistry, Saint Petersburg State University, St. Petersburg, Russia
| | - Alexey Y Timoshkin
- Institute of Chemistry, Saint Petersburg State University, St. Petersburg, Russia
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4
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Cao W, Warneke J, Wang XB. Probing the Electronic Structure of [B 10H 10] 2- Dianion Encapsulated by an Octamethylcalix[4]pyrrole Molecule. J Phys Chem A 2024; 128:3361-3369. [PMID: 38651632 DOI: 10.1021/acs.jpca.4c01736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Despite being an important closo-borate in condensed phase boron chemistry, isolated [B10H10]2- is electronically unstable and has never been detected in the gas phase. Herein, we report a successful capture of this fleeting species through binding with an octamethylcalix[4]pyrrole (omC4P) molecule to form a stable gaseous omC4P·[B10H10]2- complex and its characterizations utilizing negative ion photoelectron spectroscopy (NIPES). The recorded NIPE spectrum, contributed by both omC4P and [B10H10]2-, is deconvoluted by subtracting the omC4P contribution to yield a [B10H10]2- spectrum. The obtained [B10H10]2- spectrum consists of four major bands spanning the electron binding energy (EBE) range from 1 to 5 eV, with the EBE gaps matching excellently with the energy intervals of computed high-lying occupied molecular orbitals of the [B10H10]2- dianion. This study showcases a generic method to utilize omC4P to capture unstable multiply charged anions in the gas phase for experimental determination of their electronic structures.
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Affiliation(s)
- Wenjin Cao
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, Washington 99352, United States
| | - Jonas Warneke
- Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry, Leipzig University, Leipzig 04103, Germany
- Leibniz Institute of Surface Engineering (IOM), Permoserstraße 15, Leipzig 04318, Germany
| | - Xue-Bin Wang
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, Washington 99352, United States
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5
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Xu X, Jiang H, Wu K. Uranyl Affinity between Uranyl Cation and Different Kinds of Monovalent Anions: Density Functional Theory and Quantitative Structure-Property Relationship Model. J Phys Chem A 2024; 128:2960-2970. [PMID: 38576211 DOI: 10.1021/acs.jpca.4c00068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
In order to design effective extractants for uranium extraction from seawater, it is imperative to acquire a more comprehensive understanding of the bonding properties between the uranyl cation (UO22+) and various ligands. Therefore, we employed density functional theory to investigate the complexation reactions of UO22+ with 29 different monovalent anions (L-1), exploring both mono- and bidentate coordination. We proposed a novel concept called "uranyl affinity" (Eua) to facilitate the establishment of a standardized scale for assessing the ease or difficulty of coordination bond formation between UO22+ and diverse ligands. Furthermore, we conducted an in-depth investigation into the underlying mechanisms involved. During the process of uranyl complex [(UO2L)+] formation, lone pair electrons from the coordinating atom in L- are transferred to either the lowest unoccupied molecular degenerate orbitals 1ϕu or 1δu of the uranyl ion, which originate from the uranium atom's 5f unoccupied orbitals. In light of discussion concerning the mechanisms of coordination bond formation, quantitative structure-property relationship analyses were conducted to investigate the correlation between Eua and various structural descriptors associated with the 29 ligands under investigation. This analysis revealed distinct patterns in Eua values while identifying key influencing factors among the different ligands.
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Affiliation(s)
- Xiang Xu
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Haiyan Jiang
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Kechen Wu
- Fujian Key Laboratory of Functional Marine Sensing Materials, Minjiang University, Fuzhou 350108, China
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6
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Cao W, Wang XB. Organic Molecules Mimic Alkali Metals Enabling Spontaneous Harpoon Reactions with Halogens. Chemistry 2024; 30:e202400038. [PMID: 38287792 DOI: 10.1002/chem.202400038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 01/31/2024]
Abstract
The harpoon mechanism has been a milestone in molecular reaction dynamics. Until now, the entity from which electron harpooning occurs has been either alkali metal atoms or non-metallic analogs in their excited states. In this work, we demonstrate that a common organic molecule, octamethylcalix[4] pyrrole (omC4P), behaves just like alkali metal atoms, enabling the formation of charge-separated ionic bonding complexes with halogens omC4P+ ⋅ X- (X=F-I, SCN) via the harpoon mechanism. Their electronic structures and chemical bonding were determined by cryogenic photoelectron spectroscopy of the corresponding anions and confirmed by theoretical analyses. The omC4P+ ⋅ X- could be visualized to form from the reactants omC4P+X via electron harpooning from omC4P to X at a distance defined by the energy difference between the ionization potential of omC4P and electron affinity of X.
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Affiliation(s)
- Wenjin Cao
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P. O. Box 999, MS J7-10, Richland, WA, 99352, USA
| | - Xue-Bin Wang
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P. O. Box 999, MS J7-10, Richland, WA, 99352, USA
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7
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Wang X, Niu Z, McDowell SAC, Li Q. Triel Bonds between BH 3/C 5H 4BX and M(MDA) 2 (X = H, CN, F, CH 3, NH 2; M = Ni, Pd, Pt, MDA = Enolated Malondialdehyde) and Group 10 Transition Metal Electron Donors. Molecules 2024; 29:1602. [PMID: 38611881 PMCID: PMC11013632 DOI: 10.3390/molecules29071602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 03/30/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024] Open
Abstract
A systematic theoretical study was conducted on the triel bonds (TrB) within the BH3∙∙∙M(MDA)2 and C5H4BX∙∙∙M(MDA)2 (M = Ni, Pd, Pt, X = H, CN, F, CH3, NH2, MDA = enolated malondialdehyde) complexes, with BH3 and C5H4BX acting as the electron acceptors and the square-coordinated M(MDA)2 acting as the electron donor. The interaction energies of these systems range between -4.71 and -33.18 kcal/mol. The larger the transition metal center M, the greater the enhancement of the TrB, with σ-hole TrBs found to be stronger than π-hole TrBs. In the σ-hole TrB complex, an electron-withdrawing substituent on the C opposite to the B atom enhances the TrB, while an electron-donating substituent has little effect on the strength of TrB in the Pd and Pt complexes but enhances the TrB in the Ni-containing complexes. The van der Waals interaction plays an important role in stabilizing these binary systems, and its contribution diminishes with increasing M size. The orbital effect within these systems is largely due to charge transfer from the dz2 orbital of M into the empty pz orbital of B.
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Affiliation(s)
- Xin Wang
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, China; (X.W.); (Z.N.)
| | - Zhihao Niu
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, China; (X.W.); (Z.N.)
| | - Sean A. C. McDowell
- Department of Biological and Chemical Sciences, The University of the West Indies, Cave Hill Campus, Bridgetown BB11000, Barbados
| | - Qingzhong Li
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, China; (X.W.); (Z.N.)
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8
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Devore DP, Ellington TL, Shuford KL. Elucidating the Role of Electron-Donating Groups in Halogen Bonding. J Phys Chem A 2024; 128:1477-1490. [PMID: 38373286 DOI: 10.1021/acs.jpca.3c06894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Computational quantum chemical techniques were utilized to systematically examine how electron-donating groups affect the electronic and spectroscopic properties of halogen bond donors and their corresponding complexes. Unlike the majority of studies on halogen bonding, where electron-withdrawing groups are utilized, this work investigates the influence of electron-donating substituents within the halogen bond donors. Statistical analyses were performed on the descriptors of halogen bond donors in a prescribed set of archetype, halo-alkyne, halo-benzene, and halo-ethynyl benzene halogen bond systems. The σ-hole magnitude, binding and interaction energies, and the vibrational X···N local force constant (where X = Cl, Br, I, and At) were found to correlate very well in a monotonic and linear manner with all other properties studied. In addition, enhanced halogen bonds were found when the systems contained electron-donating groups that could form intramolecular hydrogen bonds with the electronegative belt of the halogen atom and adjacent linker features.
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Affiliation(s)
- Daniel P Devore
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798-7348, United States
| | - Thomas L Ellington
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798-7348, United States
| | - Kevin L Shuford
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798-7348, United States
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9
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Lazzari F, Mendolicchio M, Barone V. Accurate Geometries of Large Molecules by Integration of the Pisa Composite Scheme and the Templating Synthon Approach. J Phys Chem A 2024; 128:1385-1395. [PMID: 38347709 DOI: 10.1021/acs.jpca.3c08382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
An effective yet reliable computational workflow is proposed, which permits the computation of accurate geometrical structures for large flexible molecules at an affordable cost thanks to the integration of machine learning tools and DFT models together with reduced scaling computations of vibrational averaging effects. After validation of the different components of the overall strategy, a panel of molecules of biological interest have been analyzed. The results confirm that very accurate geometrical parameters can be obtained at reasonable cost for molecules including up to about 50 atoms, which are the largest ones for which comparison with high-resolution rotational spectra is possible. Since the whole computational workflow can be followed employing standard electronic structure codes, accurate results for large-sized molecules can be obtained at DFT cost also by nonspecialists.
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Affiliation(s)
- Federico Lazzari
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Marco Mendolicchio
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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10
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Weike N, Eisfeld W. The effective relativistic coupling by asymptotic representation approach for molecules with multiple relativistic atoms. J Chem Phys 2024; 160:064104. [PMID: 38341788 DOI: 10.1063/5.0191529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 01/18/2024] [Indexed: 02/13/2024] Open
Abstract
The Effective Relativistic Coupling by Asymptotic Representation (ERCAR) approach is a method to generate fully coupled diabatic potential energy surfaces (PESs) including relativistic effects, especially spin-orbit coupling. The spin-orbit coupling of a full molecule is determined only by the atomic states of selected relativistically treated atoms. The full molecular coupling effect is obtained by a diabatization with respect to asymptotic states, resulting in the correct geometry dependence of the spin-orbit effect. The ERCAR approach has been developed over the last decade and initially only for molecules with a single relativistic atom. This work presents its extension to molecules with more than a single relativistic atom using the iodine molecule as a proof-of-principle example. The theory for the general multiple atomic ERCAR approach is given. In this case, the diabatic basis is defined at the asymptote where all relativistic atoms are separated from the remaining molecular fragment. The effective spin-orbit operator is then a sum of spin-orbit operators acting on isolated relativistic atoms. PESs for the iodine molecule are developed within the new approach and it is shown that the resulting fine structure states are in good agreement with spin-orbit ab initio calculations.
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Affiliation(s)
- Nicole Weike
- Theoretische Chemie, Universität Bielefeld, Postfach 100131, D-33501 Bielefeld, Germany
| | - Wolfgang Eisfeld
- Theoretische Chemie, Universität Bielefeld, Postfach 100131, D-33501 Bielefeld, Germany
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11
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Tyagi R, Voora VK. Single-Pole Polarization Models: Rapid Evaluation of Electron Affinities of Solvated-Electron and Superatomic Molecular Anionic States. J Phys Chem Lett 2024; 15:1218-1226. [PMID: 38276789 DOI: 10.1021/acs.jpclett.3c03392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
We propose a single-parameter effective one-particle potential, termed the single-pole exchange-correlation (1p-XC), to rapidly evaluate electron affinities (EAs) of nonvalence electronic states of molecular clusters and nanoassemblies. The model combines exact-exchange and the random phase approximation (RPA) correlation potential with a single-pole approximation to model the frequency-dependent polarization function. It captures long-range static and dynamic-frequency effects in the correlation potential, with mean absolute errors of 0.06 eV for EAs of hydrated- and ammoniated-electron clusters with EA values in the range 0.24-1.77 eV. The 1p-XC approximation enables EA estimation with a computational wall-time similar to that of hybrid functionals. The model also provides a compressed-basis, which significantly reduces the rank of higher-level parameter-free one-particle Hamiltonians and further simplifies the computation of EAs. The compressed-basis approach is used to model the hybridization of superatomic molecular states of (C60)2- and (C60)3-, thereby verifying previous model Hamiltonian studies.
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Affiliation(s)
- Ritaj Tyagi
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Vamsee K Voora
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
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12
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Asplund M, Koga M, Wu YJ, Neumark DM. Time-resolved photoelectron spectroscopy of iodide-4-thiouracil cluster: The ππ* state as a doorway for electron attachment. J Chem Phys 2024; 160:054301. [PMID: 38299627 DOI: 10.1063/5.0187557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/09/2024] [Indexed: 02/02/2024] Open
Abstract
The photophysics of thiobases-nucleobases in which one or more oxygen atoms are replaced with sulfur atoms- vary greatly depending on the location of sulfonation. Not only are direct dynamics of a neutral thiobase impacted, but also the dynamics of excess electron accommodation. In this work, time-resolved photoelectron spectroscopy is used to measure binary anionic clusters of iodide and 4-thiouracil, I- · 4TU. We investigate charge transfer dynamics driven by excitation at 3.88 eV, corresponding to the lowest ππ* transition of the thiouracil, and at 4.16 eV, near the cluster vertical detachment energy. The photoexcited state dynamics are probed by photodetachment with 1.55 and 3.14 eV pulses. Excitation at 3.88 eV leads to a signal from a valence-bound ion only, indicating a charge accommodation mechanism that does not involve a dipole-bound anion as an intermediate. Excitation at 4.16 eV rapidly gives rise to dipole-bound and valence-bound ion signals, with a second rise in the valence-bound signal corresponding to the decay of the dipole-bound signal. The dynamics associated with the low energy ππ* excitation of 4-thiouracil provide a clear experimental proof for the importance of localized excitation and electron backfilling in halide-nucleobase clusters.
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Affiliation(s)
- Megan Asplund
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Masafumi Koga
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Ying Jung Wu
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Daniel M Neumark
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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13
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Harriswangler C, Lucio-Martínez F, Rodríguez-Rodríguez A, Esteban-Gómez D, Platas-Iglesias C. Unravelling the 6sp ← 6s absorption spectra of Bi(III) complexes. Dalton Trans 2024; 53:2275-2285. [PMID: 38197124 DOI: 10.1039/d3dt03744d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
We report a spectroscopic and computational study that investigates the absorption spectra of Bi(III) complexes, which often show an absorption band in the UV region (∼270-350 nm) due to 6sp ← 6s transitions. We investigated the spectra of three simple complexes, [BiCl5]2-, [BiCl6]3- and [Bi(DMSO)8]3+, which show absorption maxima at 334, 326 and 279 nm due to 3P1 ← 1S0 transitions. Theoretical calculations based on quasi-degenerate N-electron valence perturbation theory to second order (QD-NEVPT2) provide an accurate description of the absorption spectra when employing CAS(2,9) wave functions. We next investigated the absorption spectra of the [Bi(NOTA)] complex (H3NOTA = 1,4,7-triazacyclononane-1,4,7-triacetic acid), which forms ternary complexes [Bi(NOTA)X]- (X = Cl, Br or I) in the presence of excess halide in aqueous solutions. Halide binding has an important impact on the position of the 3P1 ← 1S0 transition, which shifts progressively to longer wavelengths from 282 nm ([Bi(NOTA)]) to 298 nm (X = Cl), 305 nm (X = Br) and 325 nm (X = I). Subsequent QD-NEVPT2 calculations indicate that this effect is related to the progressive stabilization of the spin-orbit free states associated with the 6s16p1 configuration on increasing the covalent character of the metal-ligand(s) bonds, rather than with significant differences in spin-orbit coupling (SOC). These studies provide valuable insight into the coordination chemistry of Bi(III), an ion with increasing interest in targeted alpha therapy due to the possible application of bismuth isotopes bismuth-212 (212Bi, t1/2 = 60.6 min) and bismuth-213 (213Bi, t1/2 = 45.6 min).
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Affiliation(s)
- Charlene Harriswangler
- Universidade da Coruña, Centro de Interdisciplinar de Química e Bioloxía (CICA) and Departamento de Química, Facultade de Ciencias, 15071, A Coruña, Galicia, Spain.
| | - Fátima Lucio-Martínez
- Universidade da Coruña, Centro de Interdisciplinar de Química e Bioloxía (CICA) and Departamento de Química, Facultade de Ciencias, 15071, A Coruña, Galicia, Spain.
| | - Aurora Rodríguez-Rodríguez
- Universidade da Coruña, Centro de Interdisciplinar de Química e Bioloxía (CICA) and Departamento de Química, Facultade de Ciencias, 15071, A Coruña, Galicia, Spain.
| | - David Esteban-Gómez
- Universidade da Coruña, Centro de Interdisciplinar de Química e Bioloxía (CICA) and Departamento de Química, Facultade de Ciencias, 15071, A Coruña, Galicia, Spain.
| | - Carlos Platas-Iglesias
- Universidade da Coruña, Centro de Interdisciplinar de Química e Bioloxía (CICA) and Departamento de Química, Facultade de Ciencias, 15071, A Coruña, Galicia, Spain.
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14
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Yssartier T, Liu L, Pardoue S, Le Questel JY, Guérard F, Montavon G, Galland N. In vivo stability of 211At-radiopharmaceuticals: on the impact of halogen bond formation. RSC Med Chem 2024; 15:223-233. [PMID: 38283213 PMCID: PMC10809332 DOI: 10.1039/d3md00579h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/22/2023] [Indexed: 01/30/2024] Open
Abstract
211At, when coupled to a targeting agent, is one of the most promising radionuclides for therapeutic applications. The main labelling approach consists in the formation of astatoaryl compounds, which often show a lack of in vivo stability. The hypothesis that halogen bond (XB) interactions with protein functional groups initiate a deastatination mechanism is investigated through radiochemical experiments and DFT modelling. Several descriptors agree on the known mechanism of iodoaryl substrates dehalogenation by iodothyronine deiodinases, supporting the higher in vivo dehalogenation of N-succinimidyl 3-[211At]astatobenzoate (SAB) conjugates in comparison with their iodinated counterparts. The guanidinium group in 3-[211At]astato-4-guanidinomethylbenzoate (SAGMB) prevents the formation of At-mediated XBs with the selenocysteine active site in iodothyronine deiodinases. The initial step of At-aryl bond dissociation is inhibited, elucidating the better in vivo stability of SAGMB conjugates compared with those of SAB. The impact of astatine's ability to form XB interactions on radiopharmaceutical degradation may not be limited to the case of aryl radiolabeling.
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Affiliation(s)
- Thibault Yssartier
- CNRS, CEISAM UMR 6230, Nantes Université F-44000 Nantes France
- CNRS, SUBATECH UMR 6457, IMT Atlantique F-44307 Nantes France
| | - Lu Liu
- CNRS, IPHC UMR 7178, Université de Strasbourg F-67037 Strasbourg France
| | - Sylvain Pardoue
- CNRS, SUBATECH UMR 6457, IMT Atlantique F-44307 Nantes France
| | | | - François Guérard
- Inserm UMR 1307, CNRS UMR 6075, CRCI2NA, Nantes Université, Université d'Angers F-44000 Nantes France
| | - Gilles Montavon
- CNRS, SUBATECH UMR 6457, IMT Atlantique F-44307 Nantes France
| | - Nicolas Galland
- CNRS, CEISAM UMR 6230, Nantes Université F-44000 Nantes France
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15
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Weike N, Viel A, Eisfeld W. Hydrogen-iodine scattering. I. Development of an accurate spin-orbit coupled diabatic potential energy model. J Chem Phys 2023; 159:244119. [PMID: 38156638 DOI: 10.1063/5.0186787] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 12/05/2023] [Indexed: 01/03/2024] Open
Abstract
The scattering of H by I is a prototypical model system for light-heavy scattering in which relativistic coupling effects must be taken into account. Scattering calculations depend strongly on the accuracy of the potential energy surface (PES) model. The methodology to obtain such an accurate PES model suitable for scattering calculations is presented, which includes spin-orbit (SO) coupling within the Effective Relativistic Coupling by Asymptotic Representation (ERCAR) approach. In this approach, the SO coupling is determined only for the atomic states of the heavy atom, and the geometry dependence of the SO effect is accounted for by a diabatization with respect to asymptotic states. The accuracy of the full model, composed of a Coulomb part and the SO model, is achieved in the following ways. For the SO model, the extended ERCAR approach is applied, which accounts for both intra-state and inter-state SO coupling, and an extended number of diabatic states are included. The corresponding coupling constants for the SO operator are obtained from experiments, which are more accurate than computed values. In the Coulomb Hamiltonian model, special attention is paid to the long range behavior and accurate c6 dispersion coefficients. The flexibility and accuracy of this Coulomb model are achieved by combining partial models for three different regions. These are merged via artificial neural networks, which also refine the model further. In this way, an extremely accurate PES model for hydrogen iodide is obtained, suitable for accurate scattering calculations.
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Affiliation(s)
- Nicole Weike
- Theoretische Chemie, Universität Bielefeld, Postfach 100131, D-33501 Bielefeld, Germany
| | - Alexandra Viel
- Univ Rennes, CNRS, IPR (Institut de Physique de Rennes)-UMR 6251, F-35000 Rennes, France
| | - Wolfgang Eisfeld
- Theoretische Chemie, Universität Bielefeld, Postfach 100131, D-33501 Bielefeld, Germany
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16
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Andress TD, Maxwell JW, McNeill AS, Stanbury DM, Dixon DA. Prediction of Aqueous Reduction Potentials of X •, ChH •, and XO • Radicals with X = Halogen and Ch = Chalcogen. J Phys Chem A 2023; 127:10600-10612. [PMID: 38085654 DOI: 10.1021/acs.jpca.3c06123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
The aqueous electron affinity and aqueous reduction potentials for F•, Cl•, Br•, I•, OH•, SH•, SeH•, TeH•, ClO•, BrO•, and IO• were calculated using electronic structure methods for explicit cluster models coupled with a self-consistent reaction field (SMD) to treat the aqueous solvent. Calculations were conducted using MP2 and correlated molecular orbital theory up to the CCSD(T)-F12b level for water tetramer clusters and MP2 for octamer cluster. Inclusion of explicit waters was found to be important for accurately predicting the redox potentials in a number of cases. The calculated reduction potentials for X• and ChH• were predicted to within ∼0.1 V of the reported literature values. Fluorine is anomalous due to abstraction of a hydrogen from one of the surrounding water molecules to form a hydroxyl radical and hydrogen fluoride, so its redox potential was calculated using only an implicit model. Larger deviations from experiment were predicted for ClO• and BrO•. These deviations are due to the free energy of solvation of the anion being too negative, as found in the pKa calculations, and that for the neutral being too positive with the current approach.
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Affiliation(s)
- Thomas Dalton Andress
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Jackson W Maxwell
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Ashley S McNeill
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - David M Stanbury
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - David A Dixon
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
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17
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Donald KJ, Pham N, Ravichandran P. Sigma Hole Potentials as Tools: Quantifying and Partitioning Substituent Effects. J Phys Chem A 2023; 127:10147-10158. [PMID: 38058158 DOI: 10.1021/acs.jpca.3c05797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Empirical substituent constants, such as the Hammett parameters, have found important utility in organic and other areas of chemistry. They are useful both in predicting the impact of substitutions on chemical processes and in rationalizing after-the-fact observations on chemical bonding and reactivity. We assess the impact of substitutions on monoiodinated benzene rings and find that the modifications that substituents induce on the electrostatic potentials at the sigma hole on the terminal I center correlate strongly with established trends of common substituents. As an alternative to the experimental procedures involved in obtaining empirically based substituent constants, the computationally determined constants based on induced electrostatic potentials offer a model for quantifying the influence of mono- and polyatomic, neutral, and ionic substituents on their compounds. A partitioning scheme is proposed that allows us to discretely separate σ and π contributions to generate quantitative measures of substituent effects.
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Affiliation(s)
- Kelling J Donald
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia 23173, United States
| | - Nam Pham
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia 23173, United States
| | - Pranav Ravichandran
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia 23173, United States
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18
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Erba A, Desmarais JK, Casassa S, Civalleri B, Donà L, Bush IJ, Searle B, Maschio L, Edith-Daga L, Cossard A, Ribaldone C, Ascrizzi E, Marana NL, Flament JP, Kirtman B. CRYSTAL23: A Program for Computational Solid State Physics and Chemistry. J Chem Theory Comput 2023; 19:6891-6932. [PMID: 36502394 PMCID: PMC10601489 DOI: 10.1021/acs.jctc.2c00958] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Indexed: 12/14/2022]
Abstract
The Crystal program for quantum-mechanical simulations of materials has been bridging the realm of molecular quantum chemistry to the realm of solid state physics for many years, since its first public version released back in 1988. This peculiarity stems from the use of atom-centered basis functions within a linear combination of atomic orbitals (LCAO) approach and from the corresponding efficiency in the evaluation of the exact Fock exchange series. In particular, this has led to the implementation of a rich variety of hybrid density functional approximations since 1998. Nowadays, it is acknowledged by a broad community of solid state chemists and physicists that the inclusion of a fraction of Fock exchange in the exchange-correlation potential of the density functional theory is key to a better description of many properties of materials (electronic, magnetic, mechanical, spintronic, lattice-dynamical, etc.). Here, the main developments made to the program in the last five years (i.e., since the previous release, Crystal17) are presented and some of their most noteworthy applications reviewed.
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Affiliation(s)
- Alessandro Erba
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Jacques K. Desmarais
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Silvia Casassa
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Bartolomeo Civalleri
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Lorenzo Donà
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Ian J. Bush
- STFC
Rutherford Appleton Laboratory, Chilton Didcot, Oxfordshire OX11 0QX, United Kingdom
| | - Barry Searle
- SFTC
Daresbury Laboratory, Daresbury, Cheshire WA4 4AD, United Kingdom
| | - Lorenzo Maschio
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Loredana Edith-Daga
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Alessandro Cossard
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Chiara Ribaldone
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Eleonora Ascrizzi
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Naiara L. Marana
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Jean-Pierre Flament
- Université
de Lille, CNRS, UMR 8523 — PhLAM — Physique des Lasers, Atomes et Molécules, 59000 Lille, France
| | - Bernard Kirtman
- Department
of Chemistry and Biochemistry, University
of California, Santa
Barbara, California 93106, United States
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19
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Herbstritt D, Tomar P, Müller R, Kaupp M, Braun T. A 2,2-Difluoroimidazolidine Derivative for Deoxyfluorination Reactions: Mechanistic Insights by Experimental and Computational Studies. Chemistry 2023; 29:e202301556. [PMID: 37341145 DOI: 10.1002/chem.202301556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/20/2023] [Accepted: 06/20/2023] [Indexed: 06/22/2023]
Abstract
A N-heterocyclic deoxyfluorinating agent SIMesF2 was synthesized by nucleophilic fluorination of N,N-1,3-dimesityl-2-chloroimidazolidinium chloride (3) at room temperature. SIMesF2 was applied to deoxyfluorinate carboxylic acids and alcohols and convert benzaldehyde into difluorotoluene. Mechanistic studies by NMR spectroscopy suggest reaction pathways of the carboxylic acid to acyl fluoride via outer-sphere fluorinations at an imidazolidinium ion by polyfluoride. DFT studies give further insight by exploring mechanistic details which distinguish the fluorination of aldehydes from that of carboxylic acids. Furthermore, a consecutive reaction sequence for the oxidation of an aldehyde followed by in situ fluorination of the generated carboxylic acid was developed.
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Affiliation(s)
- Domenique Herbstritt
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Pooja Tomar
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Robert Müller
- Institut für Chemie, Technische Universität Berlin, Theoretische Chemie/Quantenchemie, Sekr.C7, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Martin Kaupp
- Institut für Chemie, Technische Universität Berlin, Theoretische Chemie/Quantenchemie, Sekr.C7, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Thomas Braun
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
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20
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Jiang Y, Hu Z, Zhong C, Yang Y, Wang XB, Sun Z, Sun H, Liu Z, Peng P. Locking water molecules via ternary O-H⋯O intramolecular hydrogen bonds in perhydroxylated closo-dodecaborate. Phys Chem Chem Phys 2023; 25:25810-25817. [PMID: 37724455 DOI: 10.1039/d3cp03555g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
Abstract
A multitude of applications related to perhydroxylated closo-dodecaborate B12(OH)122- in the condensed phase are inseparable from the fundamental mechanisms underlying the high water orientation selectivity based on the base B12(OH)122-. Herein, we directly compare the structural evolution of water clusters, ranging from monomer to hexamer, oriented by functional groups in the bases B12H122-, B12H11OH2- and B12(OH)122- using multiple theoretical methods. A significant revelation is made regarding B12(OH)122-: each additional water molecule is locked into the intramolecular hydrogen bond B-O-H ternary ring in an embedded form. This new pattern of water cluster growth suggests that B-(H-O)⋯H-O interactions prevail over the competition from water-hydrogen bonds (O⋯H-O), distinguishing it from the behavior observed in B12H122- and B12H11OH2- bases, in which competition arises from a mixed competing model involving dihydrogen bonds (B-H⋯H-O), conventional hydrogen bonds (B-(H-O)⋯H-O) and water hydrogen bonds (O⋯H-O). Through aqueous solvation and ab initio molecular dynamics analysis, we further demonstrate the largest water clusters in the first hydrated shell with exceptional thermodynamic stability around B12(OH)122-. These findings provide a solid scientific foundation for the design of boron cluster chemistry incorporating hydroxyl-group-modified borate salts with potential implications for various applications.
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Affiliation(s)
- Yanrong Jiang
- Center for Transformative Science, ShanghaiTech University, Shanghai 201210, China.
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China.
| | - Zhubin Hu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China.
| | - Cheng Zhong
- College of Chemistry & Molecular Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Yan Yang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China.
| | - Xue-Bin Wang
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, Washington 99352, USA
| | - Zhenrong Sun
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China.
| | - Haitao Sun
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China.
| | - Zhi Liu
- Center for Transformative Science, ShanghaiTech University, Shanghai 201210, China.
| | - Peng Peng
- Center for Transformative Science, ShanghaiTech University, Shanghai 201210, China.
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21
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Andriola DM, Peterson KA. Coupled Cluster Study of the Heats of Formation of UF 6 and the Uranium Oxyhalides, UO 2X 2 (X = F, Cl, Br, I, and At). J Phys Chem A 2023; 127:7579-7585. [PMID: 37657073 DOI: 10.1021/acs.jpca.3c04420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/03/2023]
Abstract
The atomization enthalpies of the U(VI) species UF6 and the uranium oxyhalides UO2X2 (X = F, Cl, Br, I, and At) were calculated using a composite relativistic Feller-Peterson-Dixon (FPD) approach based on scalar relativistic DKH3-CCSD(T) with extrapolations to the CBS limit. The inherent multideterminant nature of the U atom was mitigated by utilizing the singly charged atomic cation in all calculations with correction back to the neutral asymptote via the accurate ionization energy of the U atom. The effects of SO coupling were recovered using full 4-component CCSD(T) with contributions due to the Gaunt Hamiltonian calculated using Dirac-Hartree-Fock. The final atomization enthalpy for UF6 (752.2 kcal/mol) was within 2.5 kcal/mol of the experimental value, but unfortunately the latter carries a ±2.4 kcal/mol uncertainty that is predominantly due to the experimental uncertainty in the formation enthalpy of the U atom. The analogous value for UO2F2 (607.6 kcal/mol) was in nearly exact agreement with the experiment, but the latter has a stated experimental uncertainty of ±4.3 kcal/mol. The FPD atomization enthalpy for UO2Cl2 (540.4 kcal/mol) was within the experimental error limit of ±5.5 kcal/mol. FPD atomization energies for the non-U-containing molecules (used for reaction enthalpies) H2O and HX (X = F, Cl, Br, I, and At) were within at most 0.3 kcal/mol of their experimental values where available. The FPD atomization enthalpies, together with FPD reaction enthalpies for two different reactions, were used to determine heats of formation for all species of this work, with estimated uncertainties of ±4 kcal/mol. The calculated heat of formation for UF6 (-511.0 kcal/mol) is within 2.5 kcal/mol of the accurately known (±0.45 kcal/mol) experimental value.
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Affiliation(s)
- Devon M Andriola
- Department of Chemistry, Washington State University, Pullman, Washington 99164-4630, United States
| | - Kirk A Peterson
- Department of Chemistry, Washington State University, Pullman, Washington 99164-4630, United States
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22
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Semidalas E, Martin JML. Correlation Consistent Basis Sets for Explicitly Correlated Theory: The Transition Metals. J Chem Theory Comput 2023; 19:5806-5820. [PMID: 37540641 PMCID: PMC10500978 DOI: 10.1021/acs.jctc.3c00506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Indexed: 08/06/2023]
Abstract
We present correlation consistent basis sets for explicitly correlated (F12) calculations, denoted VnZ(-PP)-F12-wis (n = D,T), for the d-block elements. The cc-pVDZ-F12-wis basis set is contracted to [8s7p5d2f] for the 3d-block, while its ECP counterpart for the 4d and 5d-blocks, cc-pVDZ-PP-F12-wis, is contracted to [6s6p5d2f]. The corresponding contracted sizes for cc-pVTZ(-PP)-F12-wis are [9s8p6d3f2g] for the 3d-block elements and [7s7p6d3f2g] for the 4d and 5d-block elements. Our VnZ(-PP)-F12-wis basis sets are evaluated on challenging test sets for metal-organic barrier heights (MOBH35) and group-11 metal clusters (CUAGAU-2). In F12 calculations, they are found to be about as close to the complete basis set limit as the combination of standard cc-pVnZ-F12 on main-group elements with the standard aug-cc-pV(n+1)Z(-PP) basis sets on the transition metal(s). While our basis sets are somewhat more compact than aug-cc-pV(n+1)Z(-PP), the CPU time benefit is negligible for catalytic complexes that contain only one or two transition metals among dozens of main-group elements; however, it is somewhat more significant for metal clusters.
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Affiliation(s)
- Emmanouil Semidalas
- Department of Molecular Chemistry
and Materials Science, Weizmann Institute
of Science, 7610001 Reḥovot, Israel
| | - Jan M. L. Martin
- Department of Molecular Chemistry
and Materials Science, Weizmann Institute
of Science, 7610001 Reḥovot, Israel
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23
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Liu X, Guo W, Feng H, Pang B, Wu Y. Competition between Elimination and Substitution for Ambident Nucleophiles CN - and Iodoethane Reactions in Gaseous and Aqueous Medium. J Phys Chem A 2023; 127:7373-7382. [PMID: 37639466 DOI: 10.1021/acs.jpca.3c04630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Nucleophilic substitution (SN2) and elimination (E2) reactions between ambident nucleophiles have long been considered as typical reactions in organic chemistry, and exploring the competition between the two reactions is of great importance in chemical synthesis. As a nucleophile, CN- can use its C and N atoms as the reactive centers to undergo E2 and SN2 reactions, but related research is currently limited. This study uses the CCSD(T)/pp/t//MP2/ECP/d electronic structure method to perform detailed investigations on the potential energy profiles for SN2 and E2 reactions between CN- and CH3CH2I in gaseous and aqueous media. The potential energy profiles reveal that the energy barriers for SN2 and E2 reactions with the C atom as the reactive center are consistently lower than those with the N atom, indicating that the C atom has a stronger nucleophilic ability and stronger basicity. Furthermore, the potential energy profiles in both gas and aqueous environments show that the barriers of SN2 reactions are lower than those for E2 reactions with both C and N as the attacking atom. By using the frontier molecular orbital and activation strain models to explain the interesting phenomenon, the transition from the gas phase to solution was investigated, specifically in the gas-microsolvation-water transition. The results show that water molecules reduce the nucleophilicity and basicity of CN-, while strain energy (ΔEstrain) causes a greater increase in the energy barrier for E2 reactions. This study provides new insights and perspectives on the understanding of CN- as a nucleophile in SN2 reactions and serves as theoretical guidance for organic synthesis.
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Affiliation(s)
- Xu Liu
- College of Chemistry, Liaoning University, Shenyang 110036, P. R. China
| | - Wenyu Guo
- College of Chemistry, Liaoning University, Shenyang 110036, P. R. China
| | - Huining Feng
- College of Chemistry, Liaoning University, Shenyang 110036, P. R. China
| | - Boxue Pang
- Key Laboratory of Ministry of Education on Safe Mining of Deep Metal Mines, School of Resources and Civil Engineering, Northeastern University, Shenyang 110819, China
| | - Yang Wu
- College of Chemistry, Liaoning University, Shenyang 110036, P. R. China
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24
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Stošek J, Semrád H, Mazal C, Munzarová M. Mechanistic Analysis of Alkyne Haloboration: A DFT, MP2, and DLPNO-CCSD(T) Study. J Phys Chem A 2023; 127:6135-6146. [PMID: 37489760 PMCID: PMC10405270 DOI: 10.1021/acs.jpca.3c00607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 06/23/2023] [Indexed: 07/26/2023]
Abstract
Stereocontrol of the alkyne haloboration reaction has received attention in many experimental but few theoretical studies. Here we present a detailed quantum-chemical study of mechanisms leading to Z versus E isomers of haloboration products, considering acetylene and propyne combined with BCl3, BBr3, and BI3. Calculations using B3LYP-D3, MP2, and DLPNO-CCSD(T) methods are used to study polar reactions between the alkyne and BX3 in the absence and presence of an additional halide anion whose content in the reaction mixture can be controlled experimentally. The formation of anti-haloboration products via radical mechanisms is also explored, namely, by adding BX3 to (Z)-halovinyl radical. For the anti-haloboration of propyne, the radical route is prohibited by the regiochemistry of the initiating halopropenyl radical, while the polar route is unlikely due to a competitive allene generation. In contrast, energetically accessible routes exist for both syn- and anti-bromoboration of acetylene; hence, careful control of reaction conditions is necessary to steer the stereochemical outcome. Methodologically, MP2 results correspond better to the DLPNO-CCSD(T) energies than the B3LYP-D3 results in terms of both reaction barrier heights and relative ordering of energetically close stationary points.
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25
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Schlegel HB. Charge Migration in HCCI Cations Probed by Strong Field Ionization: Time-Dependent Configuration Interaction and Vibrational Wavepacket Simulations. J Phys Chem A 2023; 127:6040-6050. [PMID: 37459461 DOI: 10.1021/acs.jpca.3c02667] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Strong field ionization of neutral iodoacetylene (HCCI) can produce a coherent superposition of the X and A cations and results in charge migration between the CC π orbital and the iodine π-type lone pair. This charge migration causes oscillations in the rate of strong field ionization of the cation to the dication that can be monitored using intense few-cycle probe pulses. The dynamics and strong field ionization of the coherent superposition the X and A states of HCCI+ have been modeled by time-dependent configuration interaction (TDCI) simulations. When the nuclei are allowed to move, the electronic wavefunctions need to be multiplied by vibrational wavefunctions. Nuclear motion has been modeled by vibrational packets moving on quadratic approximations to the potential energy surfaces for the X and A states of the cation. The overlap of the vibrational wavepackets decays in about 10-15 fs. Consequently, the oscillations in the strong field ionization decay on the same time scale. A revival of the vibrational overlap and in the oscillations of the strong field ionization is seen at 60-110 fs. TDCI simulations show that the decay and revival of the charge migration can be monitored by strong field ionization with intense 2- and 4-cycle linearly polarized 800 nm pulses. The revival is also seen with 7-cycle pulses.
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Affiliation(s)
- H Bernhard Schlegel
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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26
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Wang M, He X, Taylor M, Lorpaiboon W, Mun H, Ho J. Molecular Geometries and Vibrational Contributions to Reaction Thermochemistry Are Surprisingly Insensitive to the Choice of Basis Sets. J Chem Theory Comput 2023. [PMID: 37463146 DOI: 10.1021/acs.jctc.3c00388] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Calculation of molecular geometries and harmonic vibrational frequencies are pre-requisites for thermochemistry calculations. Contrary to conventional wisdom, this paper demonstrates that quantum chemical predictions of the thermochemistry of many gas and solution phase chemical reactions appear to be very insensitive to the choice of basis sets. For a large test set of 80 diverse organic and transition-metal-containing reactions, variations in reaction free energy based on geometries and frequencies calculated using a variety of double and triple-zeta basis sets from the Pople, Jensen, Ahlrichs, and Dunning families are typically less than 4 kJ mol-1, especially when the quasiharmonic oscillator correction is applied to mitigate the effects of low-frequency modes. Our analysis indicates that for many organic molecules and their transition states, high-level revDSD-PBEP86-D4 and DLPNO-CCSD(T)/(aug-)cc-pVTZ single-point energies usually vary by less than 2 kJ mol-1 on density functional theory geometries optimized using basis sets ranging from 6-31+G(d) to aug-pcseg-2 and aug-cc-pVTZ. In cases where these single-point energies vary significantly, indicating sensitivity of molecular geometries to the choice of basis set, there is often substantial cancellation of errors when the reaction energy or barrier is calculated. The study concludes that the choice of basis set for molecular geometry and frequencies, particularly those considered in this study, is not critical for the accuracy of thermochemistry calculations in the gas or solution phase.
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Affiliation(s)
- Minzhi Wang
- School of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Xinlan He
- School of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Mackenzie Taylor
- School of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Wanutcha Lorpaiboon
- School of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Haedam Mun
- School of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Junming Ho
- School of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
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27
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Tyagi R, Zen A, Voora VK. Quantifying the Impact of Halogenation on Intermolecular Interactions and Binding Modes of Aromatic Molecules. J Phys Chem A 2023. [PMID: 37406194 DOI: 10.1021/acs.jpca.3c02291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
Halogenation of aromatic molecules is frequently used to modulate intermolecular interactions with ramifications for optoelectronic and mechanical properties. In this work, we accurately quantify and understand the nature of intermolecular interactions in perhalogenated benzene (PHB) clusters. Using benchmark binding energies from the fixed-node diffusion Monte Carlo (FN-DMC) method, we show that generalized Kohn-Sham semicanonical projected random phase approximation (GKS-spRPA) plus approximate exchange kernel (AKX) provides reliable interaction energies with mean absolute error (MAE) of 0.23 kcal/mol. Using the GKS-spRPA+AXK method, we quantify the interaction energies of several binding modes of PHB clusters ((C6X6)n; X = F, Cl, Br, I; n = 2, 3). For a given binding mode, the interaction energies increase 3-4 times from X = F to X = I; the X-X binding modes have energies in the range of 2-4 kcal/mol, while the π-π binding mode has interaction energies in the range of 4-12 kcal/mol. SAPT-DFT-based energy decomposition analysis is then used to show that the equilibrium geometries are dictated primarily by the dispersion and exchange interactions. Finally, we test the accuracy of several dispersion-corrected density functional approximations and show that only the r2SCAN-D4 method has a low MAE and correct long-range behavior, which makes it suitable for large-scale simulations and for developing structure-function relationships of halogenated aromatic systems.
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Affiliation(s)
- Ritaj Tyagi
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Andrea Zen
- Dipartimento di Fisica Ettore Pancini, Università di Napoli Federico II, Monte S. Angelo, I-80126 Napoli, Italy
| | - Vamsee K Voora
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
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Dzięcioł B, Osadchuk I, Cukras J, Lundell J. Complexes of HXeY with HX (Y, X = F, Cl, Br, I): Symmetry-Adapted Perturbation Theory Study and Anharmonic Vibrational Analysis. Molecules 2023; 28:5148. [PMID: 37446809 DOI: 10.3390/molecules28135148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/21/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
A comprehensive analysis of the intermolecular interaction energy and anharmonic vibrations of 41 structures of the HXeY⋯HX (X, Y = F, Cl, Br, I) family of noble-gas-compound complexes for all possible combinations of Y and X was conducted. New structures were identified, and their interaction energies were studied by means of symmetry-adapted perturbation theory, up to second-order corrections: this provided insight into the physical nature of the interaction in the complexes. The energy components were discussed, in connection to anharmonic frequency analysis. The results show that the induction and dispersion corrections were the main driving forces of the interaction, and that their relative contributions correlated with the complexation effects seen in the vibrational stretching modes of Xe-H and H-X. Reasonably clear patterns of interaction were found for different structures. Our findings corroborate previous findings with better methods, and provide new data. These results suggest that the entire group of the studied complexes can be labelled as "naturally blueshifting", except for the complexes with HI.
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Affiliation(s)
- Bartosz Dzięcioł
- Department of Chemistry, University of Warsaw, 02-089 Warsaw, Poland
- Department of Physics, Faculty of Science, Graduate School of Science, The University of Tokyo, Tokyo 113-8654, Japan
| | - Irina Osadchuk
- Department of Chemistry and Biotechnology, School of Science, Tallinn University of Technology, 12618 Tallinn, Estonia
| | - Janusz Cukras
- Department of Chemistry, University of Warsaw, 02-089 Warsaw, Poland
| | - Jan Lundell
- Department of Chemistry, University of Jyväskylä, 40014 Jyväskylä, Finland
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29
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Ali E, Patel N, Patel S, Asaduzzaman A. Quantum Chemical Investigation of Snow-Mercury Interactions and Their Implication of Mercury Deposition in the Arctic. J Phys Chem A 2023; 127:2554-2563. [PMID: 36917741 DOI: 10.1021/acs.jpca.2c08551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Elemental gaseous Hg is emitted into the atmosphere through various anthropogenic and natural processes. Mercury's different species and respective transport ranges, atmospheric physical and chemical transformations, and interaction with the earth's surfaces all contribute to the global cycling of toxic mercury. Under sunlight, halogens, ozone, and nitro species oxidize the emitted elemental Hg to gaseous Hg (II) molecules, which deposit onto the snow and ice surfaces in the Arctic. To investigate the fate of deposited mercury, a quantum chemical investigation was conducted using first-principles density functional theory (DFT) to analyze the interaction between various mercury molecules and snow clusters of differing sizes. Results show that all oxidized mercury molecules: XHgY, BrHgOX, BrHgXO XHgOH, XHgO2H, and XHgNO2, with X, Y = Cl, Br, and I atoms have thermodynamically stable interactions with snow clusters. Further, the adsorption energy of all mercury molecules increases with increasing size of snow clusters. Additionally, the orientations of deposited mercury molecules on the cluster surface also influence the mercury-snow interactions.
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Affiliation(s)
- Emaan Ali
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- School of Science, Engineering and Technology, Pennsylvania State University - Harrisburg, Middletown, Pennsylvania 17057, United States
| | - Nandini Patel
- School of Science, Engineering and Technology, Pennsylvania State University - Harrisburg, Middletown, Pennsylvania 17057, United States
| | - Shrina Patel
- School of Science, Engineering and Technology, Pennsylvania State University - Harrisburg, Middletown, Pennsylvania 17057, United States
| | - Abu Asaduzzaman
- School of Science, Engineering and Technology, Pennsylvania State University - Harrisburg, Middletown, Pennsylvania 17057, United States
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30
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Niu Z, McDowell SAC, Li Q. Triel Bonds with Au Atoms as Electron Donors. Chemphyschem 2023; 24:e202200748. [PMID: 36448371 DOI: 10.1002/cphc.202200748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022]
Abstract
The novel triel bonds of BX3 (X=H, F, Cl, Br, and I) and C5 H5 B as electron acceptors and AuR2 (R=Cl and CH3 ) as an electron donor were explored. The triel bond is a primary driving force for most complexes, while the contribution from a halogen-chlorine interaction in BX3 -AuCl2 (X=Cl, Br, and I) and an iodine-Au interaction in BI3 -Au(CH3 )3 is also very important. Interestingly, the positively charged Au atom of AuCl2 can attractively bind with the holes of BX3 and C5 H5 B. The interaction energy lies in the range of 1 and 80 kcal/mol, in the order X=F<H<Cl<Br<I. In most cases, the triel bond of C5 H5 B is stronger than the triel bond of BX3 . In the formation of B-Au triel bond, electrostatic energy is not dominant, while polarization energy including orbital interaction has the largest contribution for the strongly bonded complexes and dispersion energy for the weak triel bond.
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Affiliation(s)
- Zhihao Niu
- Laboratory of Theoretical and Computational Chemistry and School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, China
| | - Sean A C McDowell
- Department of Biological and Chemical Sciences, The University of the West Indies, Cave Hill Campus, Barbados
| | - Qingzhong Li
- Laboratory of Theoretical and Computational Chemistry and School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, China
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31
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Mehta N, Martin JML. The Importance of Tight f Basis Functions for Heavy p-Block Oxides and Halides: A Parallel With Tight d functions in the Second Row. J Phys Chem A 2023; 127:2104-2112. [PMID: 36854651 PMCID: PMC10009808 DOI: 10.1021/acs.jpca.3c00544] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
It is well-known that both wave function ab initio and DFT calculations on second-row compounds exhibit anomalously slow basis set convergence unless the basis sets are augmented with additional "tight" (high-exponent) d functions, as in the cc-pV(n+d)Z and aug-cc-pV(n+d)Z basis sets. This has been rationalized as being necessary for a better description of the low-lying 3d orbital, which as the oxidation state increases sinks low enough to act as a back-donation acceptor from chalcogen and halogen lone pairs. This prompts the question whether a similar phenomenon exists for the isovalent compounds of the heavy p-block. We show that for the fourth and fifth row, this is the case, but this time for tight f functions enhancing the description of the low-lying 4f and 5f Rydberg orbitals, respectively. In the third-row heavy p block, the 4f orbitals are too far up, while the 4d orbitals are adequately covered by the basis functions already present to describe the 3d subvalence orbitals.
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Affiliation(s)
- Nisha Mehta
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 76100 Reḥovot, Israel
| | - Jan M L Martin
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 76100 Reḥovot, Israel
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32
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Bodi A, Hafliðason A, Kvaran Á. Branching ratios in the dissociative photoionization of iodomethane by photoelectron photoion coincidence. Phys Chem Chem Phys 2023; 25:7383-7393. [PMID: 36826403 DOI: 10.1039/d2cp03339a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Iodomethane yields ten fragment ions after valence photoionization, in part by multiple dissociation pathways for each, thanks to a plethora of electronic states available in the parent ion as well as in the fragments. The comprehensive breakdown diagram from 11 eV to the double ionization onset, i.e., 26.7 eV, is recorded at high resolution using double imaging photoelectron photoion coincidence spectroscopy with synchrotron vacuum ultraviolet radiation. Based on fragment ion groupings, the changing branching ratios between these groups and between fragment ions within each group, as well as ancillary thermochemistry, we provide an overview of the dissociation pathways at play. Statistical and impulsive dissociations are identified using kinetic energy release analysis. Finally, a newly observed regime change is discussed in double ionization, whereby coincident H+ + I+ formation dominates over a 4 eV photon energy range, outcompeting the normally prevailing CH3+ + I+ channel.
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Affiliation(s)
- Andras Bodi
- Laboratory for Synchrotron Radiation and Femtochemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland.
| | - Arnar Hafliðason
- Science Institute, University of Iceland, Dunhagi 3, 107 Reykjavík, Iceland
| | - Ágúst Kvaran
- Science Institute, University of Iceland, Dunhagi 3, 107 Reykjavík, Iceland
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33
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Sookhaki E, Zolghadr AR, Namazian M. The effect of various partial atomic charges on the bulk and liquid/vacuum interface properties of iodobenzene derivatives at their melting points. J Mol Graph Model 2023; 119:108400. [PMID: 36586348 DOI: 10.1016/j.jmgm.2022.108400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/04/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022]
Abstract
In this work, various atomic charge schemes including natural bond orbital (NBO), electrostatic potential based (CHELPG), and σ-hole model charges were applied in the OPLS-AA force field to investigate their effects on the thermophysical and structural properties of iodobenzene and its derivatives. Molecular dynamics simulations presented in this work show that the studied structural and thermophysical properties are in good agreement with experiments when the CHELPG charge was coupled with the OPLS-AA force field. Also, the arrangement of iodobenzene derivatives in the liquid phase was investigated via combined radial/angular distribution functions (CDFs) analyses and halogen-bonding theory. The most probable orientation of iodobenzene derivatives at the liquid/vacuum interface was assigned by atom density profile and bivariate orientational distribution maps. For all studied iodobenzene derivatives, benzene rings are oriented such that the iodine atoms tend toward the vacuum phase.
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Affiliation(s)
- Elham Sookhaki
- Department of Chemistry, Yazd University, Yazd, Iran; Department of Chemistry, Shiraz University, Shiraz, 71946-84795, Iran
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34
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Grubel K, Rosenthal WS, Autrey T, Henson NJ, Koh K, Flowers S, Blake TA. An experimental, computational, and uncertainty analysis study of the rates of iodoalkane trapping by DABCO in solution phase organic media. Phys Chem Chem Phys 2023; 25:6914-6926. [PMID: 36807434 DOI: 10.1039/d2cp05286e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
NMR spectroscopy was used to measure the rates of the first and second substitution reactions between iodoalkane (R = Me, 1-butyl) and DABCO in methanol, acetonitrile and DMSO. Most of the reactions were recorded at three different temperatures, which permitted calculation of the activation parameters from Eyring and Arrhenius plots. Additionally, the reaction rate and heat of reaction for 1-iodobutane + DABCO in acetonitrile and DMSO were also measured using calorimetry. To help interpret experimental results, ab initio calculations were performed on the reactant, product, and transition state entities to understand structures, reaction enthalpies and activation parameters. Markov chain Monte Carlo statistical sampling was used to determine a distribution of kinetic rates with respect to the uncertainties in measured concentrations and correlations between parameters imposed by a kinetics model. The reactions with 1-iodobutane are found to be slower in all cases compared to reactions under similar conditions for iodomethane. This is due to steric crowding around the reaction centre for the larger butyl group compared to methyl which results in a larger activation energy for the reaction.
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Affiliation(s)
- Katarzyna Grubel
- Pacific Northwest National Laboratory, P.O. Box 999, Mail Stop K4-13, Richland, WA 99352, USA.
| | - W Steven Rosenthal
- Pacific Northwest National Laboratory, P.O. Box 999, Mail Stop K4-13, Richland, WA 99352, USA.
| | - Tom Autrey
- Pacific Northwest National Laboratory, P.O. Box 999, Mail Stop K4-13, Richland, WA 99352, USA.
| | - Neil J Henson
- Pacific Northwest National Laboratory, P.O. Box 999, Mail Stop K4-13, Richland, WA 99352, USA. .,Department of Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Katherine Koh
- Pacific Northwest National Laboratory, P.O. Box 999, Mail Stop K4-13, Richland, WA 99352, USA.
| | - Sarah Flowers
- Pacific Northwest National Laboratory, P.O. Box 999, Mail Stop K4-13, Richland, WA 99352, USA. .,Boston Heart Diagnostics, 31 Gage St., Needham, MA 02492, USA
| | - Thomas A Blake
- Pacific Northwest National Laboratory, P.O. Box 999, Mail Stop K4-13, Richland, WA 99352, USA.
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35
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Stewart GA, Hoerner P, Debrah DA, Lee SK, Schlegel HB, Li W. Attosecond Imaging of Electronic Wave Packets. PHYSICAL REVIEW LETTERS 2023; 130:083202. [PMID: 36898109 DOI: 10.1103/physrevlett.130.083202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 11/22/2022] [Indexed: 06/18/2023]
Abstract
An electronic wave packet has significant spatial evolution besides its temporal evolution, due to the delocalized nature of composing electronic states. The spatial evolution was not previously accessible to experimental investigations at the attosecond timescale. A phase-resolved two-electron-angular-streaking method is developed to image the shape of the hole density of an ultrafast spin-orbit wave packet in the krypton cation. Furthermore, the motion of an even faster wave packet in the xenon cation is captured for the first time: An electronic hole is refilled 1.2 fs after it is produced, and the hole filling is observed on the opposite side where the hole is born.
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Affiliation(s)
- Gabriel A Stewart
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
| | - Paul Hoerner
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
| | - Duke A Debrah
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
| | - Suk Kyoung Lee
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
| | - H Bernhard Schlegel
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
| | - Wen Li
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
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36
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Liu L, Li S, Zu H, Zhang X. Unexpectedly significant stabilizing mechanism of iodous acid on iodic acid nucleation under different atmospheric conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:159832. [PMID: 36404466 DOI: 10.1016/j.scitotenv.2022.159832] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/15/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
Iodous acid (HIO2) has been shown to play a stabilizing role in the nucleation of iodic acid (HIO3) (He et al., 2021). However, the stabilization effect and specific stabilizing mechanism of HIO2 on HIO3 nucleation under different atmospheric conditions remain unclear. Therefore, we studied these two issues under different temperatures and nucleation precursor concentrations using density functional theory combined with the Atmospheric Cluster Dynamics Code. We found that HIO2 can form clusters with HIO3 via strong hydrogen bonds, halogen bonds, and proton-transfer, substantially enhancing the stability of HIO3 clusters and decreasing the energy barrier of HIO3-based cluster formation at different temperatures and nucleation precursor concentrations. The particle formation rate and cluster concentrations of HIO3-HIO2 nucleation were negatively correlated with temperature and positively correlated with HIO2 concentration. The enhancements by HIO2 on the particle formation rate and cluster concentration of HIO3 nucleation were positively correlated with temperature and HIO2 concentration. Interestingly, even at a low HIO2 concentration (1.0 × 105 molecules cm-3), the enhancement on the particle formation rate and cluster concentration of HIO3 nucleation by HIO2 were both unexpectedly up to 4.1 × 104-fold at 283 K. Therefore, HIO3-HIO2 nucleation can be extremely rapid in cold regions, and the enhancement by HIO2 can be significant, especially in warm regions even at relatively high HIO2 concentrations.
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Affiliation(s)
- Ling Liu
- Key Laboratory of Cluster Science, Ministry of Education of China, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Shuning Li
- Key Laboratory of Cluster Science, Ministry of Education of China, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China; National Supercomputer Center in Tianjin, Tianjin 300451, China
| | - Haotian Zu
- Key Laboratory of Cluster Science, Ministry of Education of China, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Xiuhui Zhang
- Key Laboratory of Cluster Science, Ministry of Education of China, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China.
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37
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Amanollahi Z, Lampe L, Bensberg M, Neugebauer J, Feldt M. On the accuracy of orbital based multi-level approaches for closed-shell transition metal chemistry. Phys Chem Chem Phys 2023; 25:4635-4648. [PMID: 36662158 DOI: 10.1039/d2cp05056k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
In this work, we investigate the accuracy of the local molecular orbital molecular orbital (LMOMO) scheme and projection-based wave function-in-density functional theory (WF-in-DFT) embedding for the prediction of reaction energies and barriers of typical reactions involving transition metals. To analyze the dependence of the accuracy on the system partitioning, we apply a manual orbital selection for LMOMO as well as the so-called direct orbital selection (DOS) for both approaches. We benchmark these methods on 30 closed shell reactions involving 16 different transition metals. This allows us to devise guidelines for the manual selection as well as settings for the DOS that provide accurate results within an error of 2 kcal mol-1 compared to local coupled cluster. To reach this accuracy, on average 55% of the occupied orbitals have to be correlated with coupled cluster for the current test set. Furthermore, we find that LMOMO gives more reliable relative energies for small embedded regions than WF-in-DFT embedding.
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Affiliation(s)
- Zohreh Amanollahi
- Leibniz Institute for Catalysis (LIKAT), Albert-Einstein-Str. 29A, 18059 Rostock, Germany.
| | - Lukas Lampe
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149 Münster, Germany
| | - Moritz Bensberg
- ETH Zürich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Johannes Neugebauer
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149 Münster, Germany
| | - Milica Feldt
- Leibniz Institute for Catalysis (LIKAT), Albert-Einstein-Str. 29A, 18059 Rostock, Germany.
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38
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Liu X, McKemmish L, Pérez-Ríos J. The performance of CCSD(T) for the calculation of dipole moments in diatomics. Phys Chem Chem Phys 2023; 25:4093-4104. [PMID: 36651174 DOI: 10.1039/d2cp05060a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This work analyzes the accuracy of the coupled cluster with single, double, and perturbative triple excitation [CCSD(T)] method for predicting dipole moments. In particular, we benchmark CCSD(T) predictions for the equilibrium bond length, vibrational frequency, and dipole moment versus accurate experimental data. As a result, we find that CCSD(T) leads to accurate dipole moments. However, in some cases, it disagrees with the experimental values, and the disagreement can not be satisfactorily explained via relativistic or multi-reference effects. Therefore, our results indicate that benchmark studies for energy and geometry properties do not accurately describe other electron density magnitudes.
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Affiliation(s)
- Xiangyue Liu
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Laura McKemmish
- School of Chemistry, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Jesús Pérez-Ríos
- Department of Physics and Astronomy, Stony Brook University, Stony Brook 11794, New York, USA. .,Institute for Advanced Computational Science, Stony Brook University, Stony Brook, NY 11794-3800, USA
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39
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Perkins MA, Tschumper GS. Characterization of competing halogen-bonding and hydrogen-bonding motifs in the acetonitrile/hydrogen iodide dimer. Chem Phys 2023. [DOI: 10.1016/j.chemphys.2023.111843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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40
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Probing the Potential Energy Profile of the I + (H 2O) 3 → HI + (H 2O) 2OH Forward and Reverse Reactions: High Level CCSD(T) Studies with Spin-Orbit Coupling Included. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020904. [PMID: 36677960 PMCID: PMC9866029 DOI: 10.3390/molecules28020904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/05/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023]
Abstract
Three different pathways for the atomic iodine plus water trimer reaction I + (H2O)3 → HI + (H2O)2OH were preliminarily examined by the DFT-MPW1K method. Related to previous predictions for the F/Cl/Br + (H2O)3 reactions, three pathways for the I + (H2O)3 reaction are linked in terms of geometry and energetics. To legitimize the results, the "gold standard" CCSD(T) method was employed to investigate the lowest-lying pathway with the correlation-consistent polarized valence basis set up to cc-pVQZ(-PP). According to the CCSD(T)/cc-pVQZ(-PP)//CCSD(T)/cc-pVTZ(-PP) results, the I + (H2O)3 → HI + (H2O)2OH reaction is predicted to be endothermic by 47.0 kcal mol-1. The submerged transition state is predicted to lie 43.7 kcal mol-1 above the separated reactants. The I···(H2O)3 entrance complex lies below the separated reactants by 4.1 kcal mol-1, and spin-orbit coupling has a significant impact on this dissociation energy. The HI···(H2O)2OH exit complex is bound by 4.3 kcal mol-1 in relation to the separated products. Compared with simpler I + (H2O)2 and I + H2O reactions, the I + (H2O)3 reaction is energetically between them in general. It is speculated that the reaction between the iodine atom and the larger water clusters may be energetically analogous to the I + (H2O)3 reaction. The iodine reaction I + (H2O)3 is connected with the analogous valence isoelectronic bromine/chlorine reactions Br/Cl + (H2O)3 but much different from the F + (H2O)3 reaction. Significant difference with other halogen systems, especially for barrier heights, are seen for the iodine systems.
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41
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Jiang Y, Cai Z, Yuan Q, Cao W, Hu Z, Sun H, Wang XB, Sun Z. Highly Structured Water Networks in Microhydrated Dodecaborate Clusters. J Phys Chem Lett 2022; 13:11787-11794. [PMID: 36516831 DOI: 10.1021/acs.jpclett.2c03537] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
We report a combined photoelectron spectroscopy and theoretical investigation of a series of size-selected hydrated closo-dodecaborate clusters B12X122-·nH2O (X = H, F, or I; n = 1-6). Distinct structural arrangements of water clusters from monomer to hexamer can be achieved by using different B12X122- bases, illustrating the evident solute specificity. Because B-H···H-O dihydrogen bonds are stronger than O···H-O hydrogen bonds in water, the added water molecules are arranged in a unified binding mode by forming highly structured water networks manipulated by B12H122-. As a comparison, the hydrated B12F122- clusters display similar water evolution for n values of 1 and 2 but different binding modes for larger clusters, while water networks in B12I122- share similarities with the free water clusters. This finding provides a consistent picture of the structural diversity of hydrogen bonding networks in microhydrated dodecaborates and a molecular-level understanding of microsolvation dynamics in aqueous borate chemistry.
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Affiliation(s)
- Yanrong Jiang
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
- Center for Transformative Science, ShanghaiTech University, Shanghai 201210, China
| | - Zhaojie Cai
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
| | - Qinqin Yuan
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, Washington 99352, United States
| | - Wenjin Cao
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, Washington 99352, United States
| | - Zhubin Hu
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
| | - Haitao Sun
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Xue-Bin Wang
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, Washington 99352, United States
| | - Zhenrong Sun
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
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42
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Robinson HT, Haakansson CT, Corkish TR, Watson PD, McKinley AJ, Wild DA. Hydrogen Bonding versus Halogen Bonding: Spectroscopic Investigation of Gas-Phase Complexes Involving Bromide and Chloromethanes. Chemphyschem 2022; 24:e202200733. [PMID: 36504309 DOI: 10.1002/cphc.202200733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/12/2022] [Accepted: 12/12/2022] [Indexed: 12/14/2022]
Abstract
Hydrogen bonding and halogen bonding are important non-covalent interactions that are known to occur in large molecular systems, such as in proteins and crystal structures. Although these interactions are important on a large scale, studying hydrogen and halogen bonding in small, gas-phase chemical species allows for the binding strengths to be determined and compared at a fundamental level. In this study, anion photoelectron spectra are presented for the gas-phase complexes involving bromide and the four chloromethanes, CH3 Cl, CH2 Cl2 , CHCl3 , and CCl4 . The stabilisation energy and electron binding energy associated with each complex are determined experimentally, and the spectra are rationalised by high-level CCSD(T) calculations to determine the non-covalent interactions binding the complexes. These calculations involve nucleophilic bromide and electrophilic bromine interactions with chloromethanes, where the binding motifs, dissociation energies and vertical detachment energies are compared in terms of hydrogen bonding and halogen bonding.
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Affiliation(s)
- Hayden T Robinson
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, 6009
| | - Christian T Haakansson
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, 6009
| | - Timothy R Corkish
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, 6009
| | - Peter D Watson
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, 6009.,Department of Chemistry, University of Oxford, South Parks Road, Oxford, United Kingdom, OX1 3QZ
| | - Allan J McKinley
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, 6009
| | - Duncan A Wild
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, 6009.,School of Science, Edith Cowan University, Joondalup, Western Australia, 6027
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43
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Ellington TL, Devore DP, Uvin G De Alwis WM, French KA, Shuford KL. Shedding Light on the Vibrational Signatures in Halogen-Bonded Graphitic Carbon Nitride Building Blocks. Chemphyschem 2022; 24:e202200812. [PMID: 36480235 DOI: 10.1002/cphc.202200812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/02/2022] [Accepted: 12/08/2022] [Indexed: 12/13/2022]
Abstract
The relative contributions of halogen and hydrogen bonding to the interaction between graphitic carbon nitride monomers and halogen bond (XB) donors containing C-X and C≡C bonds were evaluated using computational vibrational spectroscopy. Conventional probes into select vibrational stretching frequencies can often lead to disconnected results. To elucidate this behavior, local mode analyses were performed on the XB donors and complexes identified previously at the M06-2X/aVDZ-PP level of theory. Due to coupling between low and high energy C-X vibrations, the C≡C stretch is deemed a better candidate when analyzing XB complex properties or detecting XB formation. The local force constants support this conclusion, as the C≡C values correlate much better with the σ-hole magnitude than their C-X counterparts. The intermolecular local stretching force constants were also assessed, and it was found that attractive forces other than halogen bonding play a supporting role in complex formation.
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Affiliation(s)
- Thomas L Ellington
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX, 76798-7348, USA
| | - Daniel P Devore
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX, 76798-7348, USA
| | - W M Uvin G De Alwis
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX, 76798-7348, USA
| | - Kirk A French
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX, 76798-7348, USA
| | - Kevin L Shuford
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX, 76798-7348, USA
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44
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McNeill AS, Stanbury DM, Dixon DA. Absolute Hydration Free Energy of Small Anions and the Aqueous p Ka of Simple Acids. J Phys Chem A 2022; 126:9190-9206. [DOI: 10.1021/acs.jpca.2c06205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Ashley S. McNeill
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
- Department of Biology and Chemistry, Springfield College, Springfield, Massachusetts 01109, United States
| | - David M. Stanbury
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - David A. Dixon
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
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45
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Pi HC, Hu CH. Property and reactivity of polyselenides and polysulfides: a quantum chemistry study. J Sulphur Chem 2022. [DOI: 10.1080/17415993.2022.2152284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Affiliation(s)
- Hui-Chu Pi
- Department of Chemistry, National Changhua University of Education, Changhua, Taiwan
| | - Ching-Han Hu
- Department of Chemistry, National Changhua University of Education, Changhua, Taiwan
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46
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The (E, Z) Isomerization of C-methoxycarbonyl-N-aryl Chlorohydrazones. CHEMISTRY 2022. [DOI: 10.3390/chemistry4040106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Since chlorohydrazones are planar molecules, it is in principle possible to distinguish between their E and Z stereoisomers. Chlorohydrazones are known to preferentially assume the Z configuration around the C=N double bond, and their (E, Z) isomerization is almost suppressed at room temperature. The lack, or rather the difficulty, of such an isomerization has been conveniently addressed by the in-depth theoretical study of seven C-methoxycarbonyl-N-aryl chlorohydrazones (aryl = phenyl, 4-chlorophenyl, 4-bromophenyl, 4-iodophenyl, 2-chlorophenyl, 2-bromophenyl, and 2-iodophenyl). DFT ωB97M-D4/cc-pVTZ calculations of these C-methoxycarbonyl-N-aryl chlorohydrazones, supported by the XRD determination of the molecular structure, provided a complete picture of the isomerization processes in the studied compounds. The analysis of the energetics, molecular geometry, and electronic structure (the latter in the framework of the Quantum Theory of Atoms In Molecules) showed that the Z isomers are thermodynamically favored because, within the low-energy planar isomers with extensive π conjugation, the electrostatic interactions between the dipoles of the C–O, C–Cl, and N–H bonds overcome the stabilization induced by the N–H ··· O bond present in the E isomers. We confirmed that the (E, Z) isomerization occurs by the umklapp mechanism, in which the –NHAr moiety rotates in the molecular plane towards a linear C=N–N configuration and then proceeds to the other isomer. The (E, Z) isomerization is very slow at room temperature because the umklapp interconversion has high barriers (≈110 kJ/mol) despite the extended π electron delocalization present in the transition state.
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47
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Wang G, Han Q, Zhu R. Computational study on the prototropic tautomerism between simple oxo-, thio-, carbon-, aza-hydrazones, and their respective azines. J Mol Model 2022; 28:393. [DOI: 10.1007/s00894-022-05387-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 11/09/2022] [Indexed: 11/19/2022]
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48
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Stabilizing Halogen-Bonded Complex between Metallic Anion and Iodide. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27228069. [PMID: 36432170 PMCID: PMC9692347 DOI: 10.3390/molecules27228069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/15/2022] [Accepted: 11/18/2022] [Indexed: 11/22/2022]
Abstract
Halogen bonds (XBs) between metal anions and halides have seldom been reported because metal anions are reactive for XB donors. The pyramidal-shaped Mn(CO)5- anion is a candidate metallic XB acceptor with a ligand-protected metal core that maintains the negative charge and an open site to accept XB donors. Herein, Mn(CO)5- is prepared by electrospray ionization, and its reaction with CH3I in gas phase is studied using mass spectrometry and density functional theory (DFT) calculation. The product observed experimentally at m/z = 337 is assigned as [IMn(CO)4(OCCH3)]-, which is formed by successive nucleophilic substitution and reductive elimination, instead of the halogen-bonded complex (XC) CH3-I···Mn(CO)5-, because the I···Mn interaction is weak within XC and it could be a transient species. Inspiringly, DFT calculations predict that replacing CH3I with CF3I can strengthen the halogen bonding within the XC due to the electro-withdrawing ability of F. More importantly, in so doing, the nucleophilic substitution barrier can be raised significantly, ~30 kcal/mol, thus leaving the system trapping within the XC region. In brief, the combination of a passivating metal core and the introduction of an electro-withdrawing group to the halide can enable strong halogen bonding between metallic anion and iodide.
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49
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Kloo L. On closed-shell interactions between heavy main-group elements. J Comput Chem 2022; 43:1985-1996. [PMID: 36129213 PMCID: PMC9825979 DOI: 10.1002/jcc.26999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/15/2022] [Accepted: 08/15/2022] [Indexed: 01/11/2023]
Abstract
A series of di- and polymetal complexes involving closed-shell, heavy main-group atoms and ions shows a selection of special physical properties. These involve short metal-metal contacts, low entropies of formation and, most interestingly, strong Raman bands at low wavenumbers. These results together with the constitution of the coordination compounds, where the majority of electrons are assembled on the highly polarizable metal atoms and ions, experimental results have been interpreted in terms of direct, partial covalent metal-metal bonding. Previous theoretical studies have challenged this view and instead attributed the obvious attractive forces involved to secondary-type of interactions, such as dispersion. This study utilizes a multitude of theoretical tools, such as natural bond order (NBO) and natural energy decomposition analysis (NEDA), non-covalent interaction (NCI) analysis, electron localization functions (ELFs), and atoms-in-molecules (AIM) to characterize the interactions in models comprising closed-shell dimers, as well as experimentally studied ring and cage systems constituting the main reason for the hypotheses on metal-metal interactions. The results show that all experimental results can be attributed to the covalent interactions between the electron-rich, metal centers and the bridging anions in ring and cage coordination compounds of high symmetry, where the experimentally observed effects can be traced to the combination of covalent interactions between the metal centers and the anions along the edges of the ring and cage systems in combination with the cooperative effects generated by the high symmetry of these ring and cage systems.
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Affiliation(s)
- Lars Kloo
- Applied Physical Chemistry, Department of ChemistryKTH Royal Institute of TechnologyStockholmSweden
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50
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Robinson HT, Corkish TR, Haakansson CT, Watson PD, McKinley AJ, Wild DA. Spectroscopic Study of the Br - +CH 3 I→I - +CH 3 Br S N 2 Reaction. Chemphyschem 2022; 23:e202200278. [PMID: 35708114 PMCID: PMC9804238 DOI: 10.1002/cphc.202200278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/06/2022] [Indexed: 01/05/2023]
Abstract
Mass spectrometry and anion photoelectron spectroscopy have been used to study the gas-phase <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:semantics> <mml:mrow><mml:msub><mml:mi>S</mml:mi> <mml:mi>N</mml:mi></mml:msub> <mml:mn>2</mml:mn></mml:mrow> <mml:annotation>${{{\rm S}}_{{\rm N}}2}$</mml:annotation> </mml:semantics> </mml:math> reaction involving <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:semantics> <mml:msup><mml:mrow><mml:mi>B</mml:mi> <mml:mi>r</mml:mi></mml:mrow> <mml:mo>-</mml:mo></mml:msup> <mml:annotation>${{{\rm B}{\rm r}}^{-}}$</mml:annotation> </mml:semantics> </mml:math> and <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:semantics> <mml:mrow> <mml:msub><mml:mrow><mml:mi>C</mml:mi> <mml:mi>H</mml:mi></mml:mrow> <mml:mn>3</mml:mn></mml:msub> <mml:mi>I</mml:mi></mml:mrow> <mml:annotation>${{{\rm C}{\rm H}}_{3}{\rm I}}$</mml:annotation> </mml:semantics> </mml:math> . The anion photoelectron spectra associated with the reaction intermediates of this <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:semantics> <mml:mrow><mml:msub><mml:mi>S</mml:mi> <mml:mi>N</mml:mi></mml:msub> <mml:mn>2</mml:mn></mml:mrow> <mml:annotation>${{{\rm S}}_{{\rm N}}2}$</mml:annotation> </mml:semantics> </mml:math> reaction are presented. High-level CCSD(T) calculations have been utilised to investigate the reaction intermediates that may form as a result of the <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:semantics> <mml:mrow><mml:msub><mml:mi>S</mml:mi> <mml:mi>N</mml:mi></mml:msub> <mml:mn>2</mml:mn></mml:mrow> <mml:annotation>${{{\rm S}}_{{\rm N}}2}$</mml:annotation> </mml:semantics> </mml:math> reaction along various different reaction pathways, including back-side attack and front-side attack. In addition, simulated vertical detachment energies of each reaction intermediate have been calculated to rationalise the photoelectron spectra.
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Affiliation(s)
- Hayden T. Robinson
- School of Molecular SciencesThe University of Western AustraliaCrawleyWestern Australia6009
| | - Timothy R. Corkish
- School of Molecular SciencesThe University of Western AustraliaCrawleyWestern Australia6009
| | | | - Peter D. Watson
- School of Molecular SciencesThe University of Western AustraliaCrawleyWestern Australia6009,Department of ChemistryUniversity of OxfordSouth Parks RoadOxfordUnited KingdomOX1 3QZ
| | - Allan J. McKinley
- School of Molecular SciencesThe University of Western AustraliaCrawleyWestern Australia6009
| | - Duncan A. Wild
- School of Molecular SciencesThe University of Western AustraliaCrawleyWestern Australia6009,School of ScienceEdith Cowan UniversityJoondalupWestern Australia6027
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