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Calabrese M, Pizzi A, Daolio A, Beccaria R, Lo Iacono C, Scheiner S, Resnati G. Osme Bond: Geometric and Energetic Features in the Adducts between OsO 4 and Lewis Bases. Chemistry 2024; 30:e202304240. [PMID: 38258620 DOI: 10.1002/chem.202304240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 01/24/2024]
Abstract
Adducts between OsO4 and Lewis bases exert a role in important oxidation processes such as epoxidation and dihydroxylation. It has been shown that the attractive interaction driving the formation of these adducts is a σ-hole bond involving the metal as the electrophilic species; the term Osme Bond (OmB) was proposed for designating it. Here some new adducts between OsO4 and various bases have been characterized through single crystal x-ray diffraction (XRD) and computational studies (density functional theory, DFT), confirming the existence of a robust correlation between σ-hole interaction energy and deformation of the tetrahedral geometry of OsO4. Also, some adducts formed by RuO4 with nucleophiles were investigated computationally.
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Affiliation(s)
- Miriam Calabrese
- NFMLab-Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, I-20131, Milan, Italy
| | - Andrea Pizzi
- NFMLab-Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, I-20131, Milan, Italy
| | - Andrea Daolio
- NFMLab-Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, I-20131, Milan, Italy
| | - Roberta Beccaria
- NFMLab-Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, I-20131, Milan, Italy
| | - Cristina Lo Iacono
- NFMLab-Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, I-20131, Milan, Italy
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, 84322-0300, United States
| | - Giuseppe Resnati
- NFMLab-Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, I-20131, Milan, Italy
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2
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Cabezón A, Calvelo M, Granja JR, Piñeiro Á, Garcia-Fandino R. Uncovering the mechanisms of cyclic peptide self-assembly in membranes with the chirality-aware MA(R/S)TINI forcefield. J Colloid Interface Sci 2023; 642:84-99. [PMID: 37001460 DOI: 10.1016/j.jcis.2023.03.101] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/19/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023]
Abstract
Cyclic peptides (CPs) formed by alternation of D- and L-amino acids (D,L-CPs) can self-assemble into nanotubes (SCPNs) by parallel or/and antiparallel stacking. Different applications have been attributed to these nanotubes, including the disruption of lipid bilayers of specific compositions and the selective transport of ions throughout membranes. Molecular dynamics (MD) simulations have significantly contributed to understand the interaction between CPs, including the structural, dynamic and transport properties of their supramolecular aggregates. The high computational cost of atomic resolution forcefields makes them impractical for simulating the self-assembly of macromolecules, so coarse-grained (CG) models might represent a more feasible solution for this purpose. However, general CG models used for the simulation of biomolecules such as the MARTINI forcefield do not explicitly consider the non-covalent interactions leading to the formation of secondary structure patterns in proteins. This becomes particularly important in the case of CPs due to the D- and L-chirality alternation in their sequence, leading to opposite orientations of the backbone polar groups on both sides of the cyclic ring plane. In order to overcome this limitation, we have extended the MARTINI forcefield to introduce chirality in each residue of the CPs. The new parametrization, which we have called MA(R/S)TINI, reproduces the expected self-assembly patterns for several CP sequences in the presence of different membrane models, explicitly considering the chirality of the CPs and with no significant extra computational cost. Our simulations provide new mechanistic information of how these systems self-assemble in presence of different lipid scenarios, showing that the CP-CP and CP-membrane interactions are sensitive to the peptide sequence chirality. This opens the door to design new bioactive CPs based on CG-MD simulations. A web-based tool for the automatic parameterization of new CP sequences using MA(R/S)TINI, among other functionalities, is under construction (see http://cyclopep.com).
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3
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de Azevedo Santos L, Ramalho TC, Hamlin TA, Bickelhaupt FM. Intermolecular Covalent Interactions: Nature and Directionality. Chemistry 2023; 29:e202203791. [PMID: 36478415 DOI: 10.1002/chem.202203791] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/07/2022] [Accepted: 12/07/2022] [Indexed: 12/12/2022]
Abstract
Quantum chemical methods were employed to analyze the nature and the origin of the directionality of pnictogen (PnB), chalcogen (ChB), and halogen bonds (XB) in archetypal Fm Z⋅⋅⋅F- complexes (Z=Pn, Ch, X), using relativistic density functional theory (DFT) at ZORA-M06/QZ4P. Quantitative Kohn-Sham MO and energy decomposition analyses (EDA) show that all these intermolecular interactions have in common that covalence, that is, HOMO-LUMO interactions, provide a crucial contribution to the bond energy, besides electrostatic attraction. Strikingly, all these bonds are directional (i.e., F-Z⋅⋅⋅F- is approximately linear) despite, and not because of, the electrostatic interactions which, in fact, favor bending. This constitutes a breakdown of the σ-hole model. It was shown how the σ-hole model fails by neglecting both, the essential physics behind the electrostatic interaction and that behind the directionality of electron-rich intermolecular interactions. Our findings are general and extend to the neutral, weaker ClI⋅⋅⋅NH3 , HClTe⋅⋅⋅NH3 , and H2 ClSb⋅⋅⋅NH3 complexes.
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Affiliation(s)
- Lucas de Azevedo Santos
- Department of Theoretical Chemistry, Amsterdam Institute for Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Teodorico C Ramalho
- Department of Chemistry, Institute of Natural Sciences, Federal University of Lavras CEP, 37200-900, Lavras, MG, Brazil.,Center for Basic and Applied Research, University Hradec Kralove, Hradec Kralove, Czech Republic
| | - Trevor A Hamlin
- Department of Theoretical Chemistry, Amsterdam Institute for Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry, Amsterdam Institute for Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands.,Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.,Department of Chemical Sciences, University of Johannesburg Auckland Park, Johannesburg, 2006, South Africa
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4
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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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5
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Preparation of In-situ Modified Diatomite and Its Application in Papermaking. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.130582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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6
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Mo Y, Danovich D, Shaik S. The roles of charge transfer and polarization in non-covalent interactions: a perspective from ab initio valence bond methods. J Mol Model 2022; 28:274. [PMID: 36006511 DOI: 10.1007/s00894-022-05187-8] [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: 08/14/2021] [Accepted: 12/03/2021] [Indexed: 11/28/2022]
Abstract
Noncovalent interactions are ubiquitous and have been well recognized in chemistry, biology and material science. Yet, there are still recurring controversies over their natures, due to the wide range of noncovalent interaction terms. In this Essay, we employed the Valence Bond (VB) methods to address two types of interactions which recently have drawn intensive attention, i.e., the halogen bonding and the CH‧‧‧HC dihydrogen bonding. The VB methods have the advantage of interpreting molecular structures and properties in the term of electron-localized Lewis (resonance) states (structures), which thereby shed specific light on the alteration of the bonding patterns. Due to the electron localization nature of Lewis states, it is possible to define individually and measure both polarization and charge transfer effects which have different physical origins. We demonstrated that both the ab initio VB method and the block-localized wavefunction (BLW) method can provide consistent pictures for halogen bonding systems, where strong Lewis bases NH3, H2O and NMe3 partake as the halogen bond acceptors, and the halogen bond donors include dihalogen molecules and XNO2 (X = Cl, Br, I). Based on the structural, spectral, and energetic changes, we confirm the remarkable roles of charge transfer in these halogen bonding complexes. Although the weak C-H∙∙∙H-C interactions in alkane dimers and graphene sheets are thought to involve dispersion only, we show that this term embeds delicate yet important charge transfer, bond reorganization and polarization interactions.
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Affiliation(s)
- Yirong Mo
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, Greensboro, NC, 27401, USA.
| | - David Danovich
- Institute of Chemistry, The Hebrew University of Jerusalem, 9190407, Jerusalem, Israel
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, 9190407, Jerusalem, Israel.
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7
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Torii H, Kimura A, Sakai T. Nature of hydrogen-bond-enhanced halogen bonding viewed through electron density changes. Phys Chem Chem Phys 2022; 24:17951-17955. [PMID: 35861167 DOI: 10.1039/d2cp02845j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Elucidating the mechanism of how we can achieve fine tuning of intermolecular interaction strength will be helpful for designing functionally important molecules. In the present study, a theoretical analysis is conducted, by examining the electron density changes, for two halogen-bonding iodinated systems whose halogen-bond strengths have been considered to be enhanced by the presence of a hydrogen-bond donating group (termed hydrogen-bond-enhanced halogen bonding). It is shown that, contrary to the expectation obtained from the enhancement of electrostatic potential along the line extended from the C-I bond, the anisotropy of electron distribution on the iodine atom remains nearly the same. This means that the hydrogen bond and halogen bond contribute almost independently and additively to the enhancement of electrostatic potential, indicating the nature of this enhancement and, in a more general sense, the relationship between the strength and the extent of directionality of halogen bonding.
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Affiliation(s)
- Hajime Torii
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan. .,Department of Optoelectronics and Nanostructure Science, Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan
| | - Akari Kimura
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan.
| | - Takanori Sakai
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan.
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8
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Krishnapriya VU, Suresh CH. The use of electrostatic potential at nuclei in the analysis of halogen bonding. NEW J CHEM 2022. [DOI: 10.1039/d2nj00256f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular electrostatic potential data at interacting nuclei provide strong evidence of bond formation in many intermolecular halogen bonded complexes.
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Affiliation(s)
- Vilakkathala U. Krishnapriya
- Chemical Science and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram – 695019, Kerala, India
- Research Centre, University of Kerala, Thiruvananthapuram, 34, Kerala, India
| | - Cherumuttathu H. Suresh
- Chemical Science and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram – 695019, Kerala, India
- Research Centre, University of Kerala, Thiruvananthapuram, 34, Kerala, India
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9
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Schiavo E, Bhattacharyya K, Mehring M, Auer AA. Are Heavy Pnictogen-π Interactions Really "π Interactions"? Chemistry 2021; 27:14520-14526. [PMID: 34342068 PMCID: PMC8596747 DOI: 10.1002/chem.202102418] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Indexed: 11/17/2022]
Abstract
The noncovalent interactions of heavy pnictogens with π-arenes play a fundamental role in fields like crystal engineering or catalysis. The strength of such bonds is based on an interplay between dispersion and donor/acceptor interactions, and is generally attributed to the presence of π-arenes. Computational studies of the interaction between the heavy pnictogens As, Sb and Bi and cyclohexane, in comparison with previous studies on the interaction between heavy pnictogens and benzene, show that this concept probably has to be revised. A thorough analysis of all the different energetic components that play a role in these systems, carried out with state-of-the-art computational methods, sheds light on how they influence one another and the effect that their interplay has on the overall system. Furthermore, the analysis of such interactions leads us to the unexpected finding that the presence of the pnictogen compounds strongly affects the conformational equilibrium of cyclohexane, reversing the relative stability of the chair and boat-twist conformers, and thus suggesting a possible application of tuneable dispersion energy donors to stabilise the desired conformation.
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Affiliation(s)
- Eduardo Schiavo
- Department of Molecular Theory and SpectroscopyMax-Planck-Institut für KohlenforschungKaiser-Wilhelm-Platz 145470Mülheim an der RuhrGermany
| | - Kalishankar Bhattacharyya
- Department of Molecular Theory and SpectroscopyMax-Planck-Institut für KohlenforschungKaiser-Wilhelm-Platz 145470Mülheim an der RuhrGermany
| | - Michael Mehring
- Institut für Chemie, KoordinationschemieTechnische Universität ChemnitzStraße der Nationen 6209107ChemnitzGermany
| | - Alexander A. Auer
- Department of Molecular Theory and SpectroscopyMax-Planck-Institut für KohlenforschungKaiser-Wilhelm-Platz 145470Mülheim an der RuhrGermany
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10
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Chen L, Dang J, Du J, Wang C, Mo Y. Hydrogen and Halogen Bonding in Homogeneous External Electric Fields: Modulating the Bond Strengths. Chemistry 2021; 27:14042-14050. [PMID: 34319620 DOI: 10.1002/chem.202102284] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Indexed: 12/28/2022]
Abstract
Recent years have witnessed various fascinating phenomena arising from the interactions of noncovalent bonds with homogeneous external electric fields (EEFs). Here we performed a computational study to interpret the sensitivity of intrinsic bond strengths to EEFs in terms of steric effect and orbital interactions. The block-localized wavefunction (BLW) method, which combines the advantages of both ab initio valence bond (VB) theory and molecular orbital (MO) theory, and the subsequent energy decomposition (BLW-ED) approach were adopted. The sensitivity was monitored and analyzed using the induced energy term, which is the variation in each energy component along the EEF strength. Systems with single or multiple hydrogen (H) or halogen (X) bond(s) were also examined. It was found that the X-bond strength change to EEFs mainly stems from the covalency change, while generally the steric effect rules the response of H-bonds to EEFs. Furthermore, X-bonds are more sensitive to EEFs, with the key difference between H- and X-bonds lying in the charge transfer interaction. Since phenylboronic acid has been experimentally used as a smart linker in EEFs, switchable sensitivity was scrutinized with the example of the phenylboronic acid dimer, which exhibits two conformations with either antiparallel or parallel H-bonds, thereby, opposite or consistent responses to EEFs. Among the studied systems, the quadruple X-bonds in molecular capsules exhibit remarkable sensitivity, with its interaction energy increased by -95.2 kJ mol-1 at the EEF strength 0.005 a.u.
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Affiliation(s)
- Li Chen
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Jingshuang Dang
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Juan Du
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Changwei Wang
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Yirong Mo
- Department of Nanoscience, Joint School of Nanoscience & Nanoengineering, University of North Carolina at Greensboro, Greensboro, NC 27401, USA
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11
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Tarannam N, Shukla R, Kozuch S. Yet another perspective on hole interactions. Phys Chem Chem Phys 2021; 23:19948-19963. [PMID: 34514473 DOI: 10.1039/d1cp03533a] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hole interactions are known by different names depending on the key atom of the bond (halogen bond, chalcogen bond, hydrogen bond, etc.), and the geometry of the interaction (σ if in line, π if perpendicular to the Lewis acid plane). However, its origin starts with the creation of a Lewis acid by an underlying covalent bond, which forms an electrostatic depletion and a virtual antibonding orbital, which can create non-covalent interactions with Lewis bases. In this (maybe subjective) perspective, we will claim that hole interactions must be defined via the molecular orbital origin of the molecule. Under this premise we can better explore the richness of such bonding patterns. For that, we will study old, recent and new systems, trying to pinpoint some misinterpretations that are often associated with them. We will use as exemplars the triel bonds, a couple of metal complexes, a discussion on convergent σ-holes, and many cases of anti-electrostatic hole interactions.
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Affiliation(s)
- Naziha Tarannam
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 841051, Israel.
| | - Rahul Shukla
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 841051, Israel.
| | - Sebastian Kozuch
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 841051, Israel.
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12
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Frutiger A, Tanno A, Hwu S, Tiefenauer RF, Vörös J, Nakatsuka N. Nonspecific Binding-Fundamental Concepts and Consequences for Biosensing Applications. Chem Rev 2021; 121:8095-8160. [PMID: 34105942 DOI: 10.1021/acs.chemrev.1c00044] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nature achieves differentiation of specific and nonspecific binding in molecular interactions through precise control of biomolecules in space and time. Artificial systems such as biosensors that rely on distinguishing specific molecular binding events in a sea of nonspecific interactions have struggled to overcome this issue. Despite the numerous technological advancements in biosensor technologies, nonspecific binding has remained a critical bottleneck due to the lack of a fundamental understanding of the phenomenon. To date, the identity, cause, and influence of nonspecific binding remain topics of debate within the scientific community. In this review, we discuss the evolution of the concept of nonspecific binding over the past five decades based upon the thermodynamic, intermolecular, and structural perspectives to provide classification frameworks for biomolecular interactions. Further, we introduce various theoretical models that predict the expected behavior of biosensors in physiologically relevant environments to calculate the theoretical detection limit and to optimize sensor performance. We conclude by discussing existing practical approaches to tackle the nonspecific binding challenge in vitro for biosensing platforms and how we can both address and harness nonspecific interactions for in vivo systems.
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Affiliation(s)
- Andreas Frutiger
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Alexander Tanno
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Stephanie Hwu
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Raphael F Tiefenauer
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - János Vörös
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Nako Nakatsuka
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
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13
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Inscoe B, Rathnayake H, Mo Y. Role of Charge Transfer in Halogen Bonding. J Phys Chem A 2021; 125:2944-2953. [PMID: 33797922 DOI: 10.1021/acs.jpca.1c01412] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Halogen bonding has received intensive attention recently for its applications in the construction of supramolecular assemblies and crystal engineering and its implications and potentials in chemical and biological processes and rational drug design. Peculiarly, in intermolecular interactions, halogen atoms are known as electron-donating groups carrying partial negative charges in molecules due to its high electronegativity, but they can counterintuitively act as Lewis acids and bind with Lewis bases in the form of a halogen bond. The unsettling issue regarding the nature of the halogen bonding is whether the electrostatics or charge transfer interaction dominates. The recently proposed σ-hole concept nicely reinforces the role of electrostatic attraction. Also, good correlations between the halogen bonding strength and the interaction energy from the simple point-charge model have been found. This leads to the claim that there is no need to invoke the charge transfer concept in the halogen bond. But there is alternative evidence supporting the importance of charge transfer interaction. Here, we visited a series of prominent halogen bonded complexes of the types Y3C-X···Z (X = Br, I; Y = F, Cl, Br; Z = F-, Cl-, Br-, I-, NMe3) with the block-localized wave function (BLW) method at the M06-2X-D3/6-311+G(d,p) (def2-SVP for iodine) level of theory. As the simplest variant of ab initio valence bond (VB) theory, the BLW method is unique in the strict localization of electrons within interacting moieties, allowing for quantitative evaluation of the charge transfer effect on geometries, spectral properties, and energetics in halogen bonding complexes. By comparing the halogen bonding complexes with and without the charge transfer interaction, we proved that the charge transfer interaction significantly shortens the X···Z bonding distance and stretches the C-X bonds. But the shortening of the halogen bonding results in the less favorable steric effect, which is composed of Pauli repulsion, electrostatics, and electron correlation. There are approximate linear correlations between the charge transfer effect and binding energy and between bonding distance and binding energy. These correlations may lead to the illusion that the charge transfer interaction is unimportant or irrelevant, but further analyses showed that the inclusion of charge transfer is critical for the proper description of the halogen bonding, as considering only electrostatics and polarization leads to only about 45-60% of the binding strengths and much elongated bonding distances.
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Affiliation(s)
- Brandon Inscoe
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, United States
| | - Hemali Rathnayake
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, United States
| | - Yirong Mo
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, United States
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14
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15
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16
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Orangi N, Eskandari K. Fluorine as a Lewis acid: A symmetry‐adapted perturbation theory based on density functional theory and interacting quantum atoms study of noncovalent interactions in the NCF⋯NH
3
complex. J Comput Chem 2020; 41:1598-1605. [DOI: 10.1002/jcc.26202] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 03/06/2020] [Accepted: 03/18/2020] [Indexed: 11/11/2022]
Affiliation(s)
| | - Kiamars Eskandari
- Department of ChemistryIsfahan University of Technology Isfahan Iran
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17
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Critical comparison of R X⋯Y and R H⋯Y directionality in halogen and hydrogen bonds using modern computational chemistry methods. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137221] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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18
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Abstract
In this review, we provide a consistent description of noncovalent interactions, covering most groups of the Periodic Table. Different types of bonds are discussed using their trivial names. Moreover, the new name “Spodium bonds” is proposed for group 12 since noncovalent interactions involving this group of elements as electron acceptors have not yet been named. Excluding hydrogen bonds, the following noncovalent interactions will be discussed: alkali, alkaline earth, regium, spodium, triel, tetrel, pnictogen, chalcogen, halogen, and aerogen, which almost covers the Periodic Table entirely. Other interactions, such as orthogonal interactions and π-π stacking, will also be considered. Research and applications of σ-hole and π-hole interactions involving the p-block element is growing exponentially. The important applications include supramolecular chemistry, crystal engineering, catalysis, enzymatic chemistry molecular machines, membrane ion transport, etc. Despite the fact that this review is not intended to be comprehensive, a number of representative works for each type of interaction is provided. The possibility of modeling the dissociation energies of the complexes using different models (HSAB, ECW, Alkorta-Legon) was analyzed. Finally, the extension of Cahn-Ingold-Prelog priority rules to noncovalent is proposed.
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19
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Sarr S, Graton J, Montavon G, Pilmé J, Galland N. On the Interplay between Charge-Shift Bonding and Halogen Bonding. Chemphyschem 2020; 21:240-250. [PMID: 31793159 DOI: 10.1002/cphc.201901023] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/29/2019] [Indexed: 01/11/2023]
Abstract
The nature of halogen-bond interactions has been analysed from the perspective of the astatine element, which is potentially the strongest halogen-bond donor. Relativistic quantum calculations on complexes formed between halide anions and a series of Y3 C-X (Y=F to X, X=I, At) halogen-bond donors disclosed unexpected trends, e. g., At3 C-At revealing a weaker donating ability than I3 C-I despite a stronger polarizability. All the observed peculiarities have their origin in a specific component of C-Y bonds: the charge-shift bonding. Descriptors of the Quantum Chemical Topology show that the halogen-bond strength can be quantitatively anticipated from the magnitude of charge-shift bonding operating in Y3 C-X. The charge-shift mechanism weakens the ability of the halogen atom X to engage in halogen bonds. This outcome provides rationales for outlier halogen-bond complexes, which are at variance with the consensus that the halogen-bond strength scales with the polarizability of the halogen atom.
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Affiliation(s)
- Serigne Sarr
- CEISAM, UMR CNRS 6230, Université de Nantes, 44000, Nantes, France
| | - Jérôme Graton
- CEISAM, UMR CNRS 6230, Université de Nantes, 44000, Nantes, France
| | - Gilles Montavon
- SUBATECH, UMR CNRS 6457 IMT Atlantique, 44307, Nantes, France
| | - Julien Pilmé
- Laboratoire de Chimie Théorique, UMR CNRS 7616, Sorbonne Université, 75005, Paris, France
| | - Nicolas Galland
- CEISAM, UMR CNRS 6230, Université de Nantes, 44000, Nantes, France
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20
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van der Lubbe SCC, Fonseca Guerra C. The Nature of Hydrogen Bonds: A Delineation of the Role of Different Energy Components on Hydrogen Bond Strengths and Lengths. Chem Asian J 2019; 14:2760-2769. [PMID: 31241855 PMCID: PMC6771679 DOI: 10.1002/asia.201900717] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Indexed: 12/04/2022]
Abstract
Hydrogen bonds are a complex interplay between different energy components, and their nature is still subject of an ongoing debate. In this minireview, we therefore provide an overview of the different perspectives on hydrogen bonding. This will be done by discussing the following individual energy components: 1) electrostatic interactions, 2) charge-transfer interactions, 3) π-resonance assistance, 4) steric repulsion, 5) cooperative effects, 6) dispersion interactions and 7) secondary electrostatic interactions. We demonstrate how these energetic factors are essential in a correct description of the hydrogen bond, and discuss several examples of systems whose energetic and geometrical features are not captured by easy-to-use predictive models.
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Affiliation(s)
- Stephanie C. C. van der Lubbe
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale ModelingVrije Universiteit AmsterdamDe Boelelaan 10831081HVAmsterdamThe Netherlands
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale ModelingVrije Universiteit AmsterdamDe Boelelaan 10831081HVAmsterdamThe Netherlands
- Leiden Institute of Chemistry, Gorlaeus LaboratoriesLeiden UniversityEinsteinweg 552333 CDLeidenThe Netherlands
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21
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Orangi N, Eskandari K, Thacker JCR, Popelier PLA. Directionality of Halogen Bonds: An Interacting Quantum Atoms (IQA) and Relative Energy Gradient (REG) Study. Chemphyschem 2019; 20:1922-1930. [DOI: 10.1002/cphc.201900250] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/23/2019] [Indexed: 01/16/2023]
Affiliation(s)
- Nasim Orangi
- Department of ChemistryIsfahan University of Technology Isfahan 84156-83111 Iran
| | - Kiamars Eskandari
- Department of ChemistryIsfahan University of Technology Isfahan 84156-83111 Iran
| | - Joseph C. R. Thacker
- Manchester Institute of Biotechnology (MIB) 131 Princess Street M1 7DN Great Britain
- School of ChemistryUniversity of Manchester Oxford Road Manchester M13 9PL Great Britain
| | - Paul L. A. Popelier
- Manchester Institute of Biotechnology (MIB) 131 Princess Street M1 7DN Great Britain
- School of ChemistryUniversity of Manchester Oxford Road Manchester M13 9PL Great Britain
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22
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Wang C, Mo Y. Classical Electrostatic Interaction Is the Origin for Blue-Shifting Halogen Bonds. Inorg Chem 2019; 58:8577-8586. [DOI: 10.1021/acs.inorgchem.9b00875] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Changwei Wang
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an 710119, China
| | - Yirong Mo
- Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008, United States
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23
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Wang C, Danovich D, Chen H, Shaik S. Oriented External Electric Fields: Tweezers and Catalysts for Reactivity in Halogen-Bond Complexes. J Am Chem Soc 2019; 141:7122-7136. [PMID: 30945542 DOI: 10.1021/jacs.9b02174] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This theoretical study establishes ways of controlling and enabling an uncommon chemical reaction, the displacement reaction, B:---(X-Y) → (B-X)+ + :Y-, which is nascent from a B:---(X-Y) halogen bond (XB) by nucleophilic attack of the base, B:, on the halogen, X. In most of the 14 cases examined, these reactions possess high barriers either in the gas phase (where the X-Y bond dissociates to radicals) or in solvents such as CH2Cl2 and CH3CN (which lead to endothermic processes). Thus, generally, the XB species are trapped in deep minima, and their reactions are not allowed without catalysis. However, when an oriented-external electric field (OEEF) is directed along the B---X---Y reaction axis, the field acts as electric tweezers that orient the XB along the field's axis, and intensely catalyze the process, by tens of kcal/mol, thus rendering the reaction allowed. Flipping the OEEF along the reaction axis inhibits the reaction and weakens the interaction of the XB. Furthermore, at a critical OEEF, each XB undergoes spontaneous and barrier-free reaction. As such, OEEF achieves quite tight control of the structure and reactivity of XB species. Valence bond modeling is used to elucidate the means whereby OEEFs exert their control.
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Affiliation(s)
- Chao Wang
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 9190407 , Israel.,Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , P. R. China
| | - David Danovich
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 9190407 , Israel
| | - Hui Chen
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , P. R. China
| | - Sason Shaik
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 9190407 , Israel
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24
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Abstract
The intrinsic bonding nature of λ 3 -iodanes was investigated to determine where its hypervalent bonds fit along the spectrum between halogen bonding and covalent bonding. Density functional theory with an augmented Dunning valence triple zeta basis set ( ω B97X-D/aug-cc-pVTZ) coupled with vibrational spectroscopy was utilized to study a diverse set of 34 hypervalent iodine compounds. This level of theory was rationalized by comparing computational and experimental data for a small set of closely-related and well-studied iodine molecules and by a comparison with CCSD(T)/aug-cc-pVTZ results for a subset of the investigated iodine compounds. Axial bonds in λ 3 -iodanes fit between the three-center four-electron bond, as observed for the trihalide species IF 2 − and the covalent FI molecule. The equatorial bonds in λ 3 -iodanes are of a covalent nature. We explored how the equatorial ligand and axial substituents affect the chemical properties of λ 3 -iodanes by analyzing natural bond orbital charges, local vibrational modes, the covalent/electrostatic character, and the three-center four-electron bonding character. In summary, our results show for the first time that there is a smooth transition between halogen bonding → 3c–4e bonding in trihalides → 3c–4e bonding in hypervalent iodine compounds → covalent bonding, opening a manifold of new avenues for the design of hypervalent iodine compounds with specific properties.
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25
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Wang C, Aman Y, Ji X, Mo Y. Tetrel bonding interaction: an analysis with the block-localized wavefunction (BLW) approach. Phys Chem Chem Phys 2019; 21:11776-11784. [DOI: 10.1039/c9cp01710k] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this study, fifty-one iconic tetrel bonding complexes were studied using the block localized wave function (BLW) method which can derive the self-consistent wavefunction for an electron-localized (diabatic) state where charge transfer is strictly deactivated.
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Affiliation(s)
- Changwei Wang
- Key Laboratory for Macromolecular Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
- Xi'an 710119
- China
| | - Yama Aman
- Department of Chemistry
- Western Michigan University
- Kalamazoo
- USA
| | - Xiaoxi Ji
- Department of Chemistry
- Western Michigan University
- Kalamazoo
- USA
| | - Yirong Mo
- Department of Chemistry
- Western Michigan University
- Kalamazoo
- USA
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26
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Ibrahim MAA, Safy MEA. A new insight for chalcogen bonding based on Point-of-Charge approach. PHOSPHORUS SULFUR 2018. [DOI: 10.1080/10426507.2018.1528255] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Mahmoud A. A. Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Mohamed E. A. Safy
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
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27
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Wang C, Danovich D, Shaik S, Wu W, Mo Y. Attraction between electrophilic caps: A counterintuitive case of noncovalent interactions. J Comput Chem 2018; 40:1015-1022. [DOI: 10.1002/jcc.25566] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/03/2018] [Accepted: 07/29/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Changwei Wang
- School of Chemistry & Chemical EngineeringShaanxi Normal University Xi'an 710119 China
| | - David Danovich
- Institute of ChemistryThe Hebrew University Jerusalem 91904 Israel
| | - Sason Shaik
- Institute of ChemistryThe Hebrew University Jerusalem 91904 Israel
| | - Wei Wu
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical EngineeringXiamen University Xiamen 360015 China
| | - Yirong Mo
- Department of ChemistryWestern Michigan University Kalamazoo Michigan 49008
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28
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Bresien J, Hering-Junghans C, Schulz A, Thomas M, Villinger A. Reactivity of TerN(SiMe3)BiCl2—Synthesis of an Aminobismuthenium Cation and TerN(SiMe3)Bi(N3)2. Organometallics 2018. [DOI: 10.1021/acs.organomet.8b00318] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jonas Bresien
- Abteilung Anorganische Chemie, Institut für Chemie, Universität Rostock, Albert-Einstein-Str. 3a, 18059 Rostock, Germany
| | - Christian Hering-Junghans
- Abteilung Anorganische Chemie, Institut für Chemie, Universität Rostock, Albert-Einstein-Str. 3a, 18059 Rostock, Germany
| | - Axel Schulz
- Abteilung Anorganische Chemie, Institut für Chemie, Universität Rostock, Albert-Einstein-Str. 3a, 18059 Rostock, Germany
- Materialdesign, Leibniz-Institut für Katalyse an der Universität Rostock, Albert-Einstein-Str. 29a, 18059 Rostock, Germany
| | - Max Thomas
- Abteilung Anorganische Chemie, Institut für Chemie, Universität Rostock, Albert-Einstein-Str. 3a, 18059 Rostock, Germany
| | - Alexander Villinger
- Abteilung Anorganische Chemie, Institut für Chemie, Universität Rostock, Albert-Einstein-Str. 3a, 18059 Rostock, Germany
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29
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Krasowska M, Schneider WB, Mehring M, Auer AA. High-Level Ab Initio Calculations of Intermolecular Interactions: Heavy Main-Group Element π-Interactions. Chemistry 2018; 24:10238-10245. [PMID: 29718544 DOI: 10.1002/chem.201801758] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Indexed: 01/24/2023]
Abstract
This work reports high-level ab initio calculations and a detailed analysis on the nature of intermolecular interactions of heavy main-group element compounds and π systems. For this purpose we have chosen a set of benchmark molecules of the form MR3 , in which M=As, Sb, or Bi, and R=CH3 , OCH3 , or Cl. Several methods for the description of weak intermolecular interactions are benchmarked including DFT-D, DFT-SAPT, MP2, and high-level coupled cluster methods in the DLPNO-CCSD(T) approximation. Using local energy decomposition (LED) and an analysis of the electron density, details of the nature of this interaction are unraveled. The results yield insight into the nature of dispersion and donor-acceptor interactions in this type of system, including systematic trends in the periodic table, and also provide a benchmark for dispersion interactions in heavy main-group element compounds.
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Affiliation(s)
- Małgorzata Krasowska
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstraße 34-36, 45470, Mülheim an der Ruhr, Germany.,Present address: Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 2, 45470, Mülheim an der Ruhr, Germany
| | - Wolfgang B Schneider
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstraße 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Michael Mehring
- Technische Universität Chemnitz, Straße der Nationen 62, 09111, Chemnitz, Germany
| | - Alexander A Auer
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstraße 34-36, 45470, Mülheim an der Ruhr, Germany.,Present address: Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 2, 45470, Mülheim an der Ruhr, Germany
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30
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Mao Y, Ge Q, Horn PR, Head-Gordon M. On the Computational Characterization of Charge-Transfer Effects in Noncovalently Bound Molecular Complexes. J Chem Theory Comput 2018; 14:2401-2417. [PMID: 29614855 DOI: 10.1021/acs.jctc.7b01256] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Charge-transfer (CT) is an important binding force in the formation of intermolecular complexes, and there have been a variety of theoretical models proposed to quantify this effect. These approaches, which typically rely on a definition of a "CT-free" state based on a partition of the system, sometimes yield significantly different results for a given intermolecular complex. Two widely used definitions of the "CT-free" state, the absolutely localized molecular orbitals (ALMO) method (where only on-fragment orbital mixings are permitted) and the constrained density functional theory (CDFT) approach (where fragment electron populations are fixed), are carefully examined in this work. Natural bond orbital (NBO) and the regularized symmetry-adapted perturbation theory (SAPT) are also briefly considered. Results for the ALMO and CDFT definitions of CT are compared on a broad range of model systems, including hydrogen-bonding systems, borane complexes, metal-carbonyl complexes, and complexes formed by water and metal cations. For most of these systems, CDFT yields a much smaller equilibrium CT energy compared to that given by the ALMO-based definition. This is mainly because the CDFT population constraint does not fully inhibit CT, which means that the CDFT "CT-free" state is in fact CT-contaminated. Examples of this contamination include (i) matching forward and backward donation (e.g., formic acid dimer) and (ii) unidirectional CT without changing fragment populations. The magnitude of the latter effect is quantified in systems such as the water dimer by employing a 3-space density constraint in addition to the orbital constraint. Furthermore, by means of the adiabatic EDA, it is shown that several observable effects of CT, such as the "pyramidalization" of the planar BH3 molecule upon the complexation with Lewis bases, already appear on the "CT-free" CDFT surface. These results reveal the essential distinctions between the ALMO and CDFT definitions of CT and suggest that the former is more consistent with accepted understanding of the role of CT in intermolecular binding.
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Affiliation(s)
- Yuezhi Mao
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry , University of California at Berkeley , Berkeley , California 94720 , United States
| | - Qinghui Ge
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry , University of California at Berkeley , Berkeley , California 94720 , United States.,Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Paul R Horn
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry , University of California at Berkeley , Berkeley , California 94720 , United States
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry , University of California at Berkeley , Berkeley , California 94720 , United States.,Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
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31
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Bouza AA, Swanson HC, Smolen KA, VanDine AL, Taracila MA, Romagnoli C, Caselli E, Prati F, Bonomo RA, Powers RA, Wallar BJ. Structure-Based Analysis of Boronic Acids as Inhibitors of Acinetobacter-Derived Cephalosporinase-7, a Unique Class C β-Lactamase. ACS Infect Dis 2018; 4:325-336. [PMID: 29144724 DOI: 10.1021/acsinfecdis.7b00152] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Acinetobacter baumannii is a multidrug resistant pathogen that infects more than 12 000 patients each year in the US. Much of the resistance to β-lactam antibiotics in Acinetobacter spp. is mediated by class C β-lactamases known as Acinetobacter-derived cephalosporinases (ADCs). ADCs are unaffected by clinically used β-lactam-based β-lactamase inhibitors. In this study, five boronic acid transition state analog inhibitors (BATSIs) were evaluated for inhibition of the class C cephalosporinase ADC-7. Our goal was to explore the properties of BATSIs designed to probe the R1 binding site. Ki values ranged from low micromolar to subnanomolar, and circular dichroism (CD) demonstrated that each inhibitor stabilizes the β-lactamase-inhibitor complexes. Additionally, X-ray crystal structures of ADC-7 in complex with five inhibitors were determined (resolutions from 1.80 to 2.09 Å). In the ADC-7/CR192 complex, the BATSI with the lowest Ki (0.45 nM) and greatest Δ Tm (+9 °C), a trifluoromethyl substituent, interacts with Arg340. Arg340 is unique to ADCs and may play an important role in the inhibition of ADC-7. The ADC-7/BATSI complexes determined in this study shed light into the unique recognition sites in ADC enzymes and also offer insight into further structure-based optimization of these inhibitors.
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Affiliation(s)
- Alexandra A. Bouza
- Department of Chemistry, Grand Valley State University, 1 Campus Drive, Allendale, Michigan 49401, United States
| | - Hollister C. Swanson
- Department of Chemistry, Grand Valley State University, 1 Campus Drive, Allendale, Michigan 49401, United States
| | - Kali A. Smolen
- Department of Chemistry, Grand Valley State University, 1 Campus Drive, Allendale, Michigan 49401, United States
| | - Alison L. VanDine
- Department of Chemistry, Grand Valley State University, 1 Campus Drive, Allendale, Michigan 49401, United States
| | - Magdalena A. Taracila
- Research
Service, Louis Stokes Cleveland Department of Veterans Affairs Medical
Center, 10701 East Boulevard, Cleveland, Ohio 44106, United States
- Departments of Medicine, Pharmacology, Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Chiara Romagnoli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Emilia Caselli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Fabio Prati
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Robert A. Bonomo
- Research
Service, Louis Stokes Cleveland Department of Veterans Affairs Medical
Center, 10701 East Boulevard, Cleveland, Ohio 44106, United States
- Departments of Medicine, Pharmacology, Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Rachel A. Powers
- Department of Chemistry, Grand Valley State University, 1 Campus Drive, Allendale, Michigan 49401, United States
| | - Bradley J. Wallar
- Department of Chemistry, Grand Valley State University, 1 Campus Drive, Allendale, Michigan 49401, United States
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32
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Mao Y, Horn PR, Head-Gordon M. Energy decomposition analysis in an adiabatic picture. Phys Chem Chem Phys 2018; 19:5944-5958. [PMID: 28176997 DOI: 10.1039/c6cp08039a] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Energy decomposition analysis (EDA) of electronic structure calculations has facilitated quantitative understanding of diverse intermolecular interactions. Nevertheless, such analyses are usually performed at a single geometry and thus decompose a "single-point" interaction energy. As a result, the influence of the physically meaningful EDA components on the molecular structure and other properties are not directly obtained. To address this gap, the absolutely localized molecular orbital (ALMO)-EDA is reformulated in an adiabatic picture, where the frozen, polarization, and charge transfer energy contributions are defined as energy differences between the stationary points on different potential energy surfaces (PESs), which are accessed by geometry optimizations at the frozen, polarized and fully relaxed levels of density functional theory (DFT). Other molecular properties such as vibrational frequencies can thus be obtained at the stationary points on each PES. We apply the adiabatic ALMO-EDA to different configurations of the water dimer, the water-Cl- and water-Mg2+/Ca2+ complexes, metallocenes (Fe2+, Ni2+, Cu2+, Zn2+), and the ammonia-borane complex. This method appears to be very useful for unraveling how physical effects such as polarization and charge transfer modulate changes in molecular properties induced by intermolecular interactions. As an example of the insight obtained, we find that a linear hydrogen bond geometry for the water dimer is preferred even without the presence of polarization and charge transfer, while the red shift in the OH stretch frequency is primarily a charge transfer effect; by contrast, a near-linear geometry for the water-chloride hydrogen bond is achieved only when charge transfer is allowed.
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Affiliation(s)
- Yuezhi Mao
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, CA 94720, USA.
| | - Paul R Horn
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, CA 94720, USA.
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, CA 94720, USA. and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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33
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Oliveira V, Kraka E, Cremer D. The intrinsic strength of the halogen bond: electrostatic and covalent contributions described by coupled cluster theory. Phys Chem Chem Phys 2018; 18:33031-33046. [PMID: 27886325 DOI: 10.1039/c6cp06613e] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
36 halogen-bonded complexes YXARm (X: F, Cl, Br; Y: donor group; ARm acceptor group) have been investigated at the CCSD(T)/aug-cc-pVTZ level of theory. Binding energies, geometries, NBO charges, charge transfer, dipole moments, electrostatic potential, electron and energy density distributions, difference density distributions, vibrational frequencies, local stretching and bending force constants, and relative bond strength orders n have been calculated and used to order the halogen bonds according to their intrinsic strength. Halogen bonding is found to arise from electrostatic and strong covalent contributions. It can be strengthened by H-bonding or lone pair delocalization. The covalent character of a halogen bond increases in the way 3c-4e (three-center-four-electron) bonding becomes possible. One can characterize halogen bonds by their percentage of 3c-4e bonding. FCl-phosphine complexes can form relatively strong halogen bonds provided electronegative substituents increase the covalent contributions in form of 3c-4e halogen bonding. Binding energies between 1 and 45 kcal mol-1 are calculated, which reflects the large variety in halogen bonding.
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Affiliation(s)
- Vytor Oliveira
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas 75275-0314, USA.
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas 75275-0314, USA.
| | - Dieter Cremer
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas 75275-0314, USA.
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34
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Ang SJ, Mak AM, Sullivan MB, Wong MW. Site specificity of halogen bonding involving aromatic acceptors. Phys Chem Chem Phys 2018. [DOI: 10.1039/c7cp08343b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Based on Cambridge structural database survey and quantum chemical studies, aromatic halogen bond (XB) acceptors are found to have unique pattern of XB binding sites and rim specificity.
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Affiliation(s)
- Shi Jun Ang
- NUS Graduate School for Integrative Sciences and Engineering
- Centre for Life Sciences
- Singapore 117456
- Singapore
- Institute of High Performance Computing
| | - Adrian M. Mak
- Institute of High Performance Computing
- Singapore 138632
- Singapore
| | - Michael B. Sullivan
- Institute of High Performance Computing
- Singapore 138632
- Singapore
- Department of Chemistry
- National University of Singapore
| | - Ming Wah Wong
- NUS Graduate School for Integrative Sciences and Engineering
- Centre for Life Sciences
- Singapore 117456
- Singapore
- Department of Chemistry
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35
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Oliveira V, Kraka E. Systematic Coupled Cluster Study of Noncovalent Interactions Involving Halogens, Chalcogens, and Pnicogens. J Phys Chem A 2017; 121:9544-9556. [PMID: 29154546 DOI: 10.1021/acs.jpca.7b10196] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The noncovalent interactions of 32 complexes involving pnicogens, chalcogens, and halogens atoms were investigated at the CCSD(T)/aug-cc-pVTZ level of theory. Two different types of complexes could be distinguished on the basis of geometric parameters, electron difference densities, and the charge transfer mechanisms associated with each type. In the type I conformation, the monomers adopt a skewed orientation allowing charge to be transfer between both monomers, whereas in the type II conformation the monomers adopt a linear arrangement, maximizing charge transfer in only one direction. Type I complexes involving the interaction between pnicogens and chalcogens cannot be unambiguously defined as chalcogen or pnicogen bonds, they are an admixture of both. The charge transfer dependence on the conformation adopted by the complexes described in this work can serve as a novel conformationally driven design concept for materials.
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Affiliation(s)
- Vytor Oliveira
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University , 3215 Daniel Ave, Dallas, Texas 75275-0314, United States
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University , 3215 Daniel Ave, Dallas, Texas 75275-0314, United States
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36
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Moore KB, Sadeghian K, Sherrill CD, Ochsenfeld C, Schaefer HF. C-H···O Hydrogen Bonding. The Prototypical Methane-Formaldehyde System: A Critical Assessment. J Chem Theory Comput 2017; 13:5379-5395. [PMID: 29039941 DOI: 10.1021/acs.jctc.7b00753] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Distinguishing the functionality of C-H···O hydrogen bonds (HBs) remains challenging, because their properties are difficult to quantify reliably. Herein, we present a study of the model methane-formaldehyde complex (MFC). Six stationary points on the MFC potential energy surface (PES) were obtained at the CCSD(T)/ANO2 level. The CCSDT(Q)/CBS interaction energies of the conformers range from only -1.12 kcal mol-1 to -0.33 kcal mol-1, denoting a very flat PES. Notably, only the lowest energy stationary point (MFC1) corresponds to a genuine minimum, whereas all other stationary points-including the previously studied ideal case of ae(C-H···O) = 180°-exhibit some degree of freedom that leads to MFC1. Despite the flat PES, we clearly see that the HB properties of MFC1 align with those of the prototypical water dimer O-H···O HB. Each HB property generally becomes less prominent in the higher-energy conformers. Only the MFC1 conformer prominently exhibits (1) elongated C-H donor bonds, (2) attractive C-H···O═C interactions, (3) n(O) → σ*(C-H) hyperconjugation, (4) critical points in the electron density from Bader's method and from the noncovalent interactions method, (5) positively charged donor hydrogen, and (6) downfield NMR chemical shifts and nonzero 2J(CM-HM···OF) coupling constants. Based on this research, some issues merit further study. The flat PES hinders reliable determinations of the HB-induced shifts of the C-H stretches; a similarly difficult challenge is observed for the experiment. The role of charge transfer in HBs remains an intriguing open question, although our BLW and NBO computations suggest that it is relevant to the C-H···O HB geometries. These issues notwithstanding, the prominence of the HB properties in MFC1 serves as clear evidence that the MFC is predominantly bound by a C-H···O HB.
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Affiliation(s)
- Kevin B Moore
- Center for Computational Quantum Chemistry, University of Georgia , Athens, Georgia 30602, United States
| | - Keyarash Sadeghian
- Department of Chemistry, Ludwig-Maximilians University (LMU) , Munich D-81377, Germany
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Christian Ochsenfeld
- Department of Chemistry, Ludwig-Maximilians University (LMU) , Munich D-81377, Germany
| | - Henry F Schaefer
- Center for Computational Quantum Chemistry, University of Georgia , Athens, Georgia 30602, United States
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37
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Oliveira V, Cremer D, Kraka E. The Many Facets of Chalcogen Bonding: Described by Vibrational Spectroscopy. J Phys Chem A 2017; 121:6845-6862. [PMID: 28782954 DOI: 10.1021/acs.jpca.7b06479] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A diverse set of 100 chalcogen-bonded complexes comprising neutral, cationic, anionic, divalent, and double bonded chalcogens has been investigated using ωB97X-D/aug-cc-pVTZ to determine geometries, binding energies, electron and energy density distributions, difference density distributions, vibrational frequencies, local stretching force constants, and associated bond strength orders. The accuracy of ωB97X-D was accessed by CCSD(T)/aug-cc-pVTZ calculations of a subset of 12 complexes and by the CCSD(T)/aug-cc-pVTZ //ωB97X-D binding energies of 95 complexes. Most of the weak chalcogen bonds can be rationalized on the basis of electrostatic contributions, but as the bond becomes stronger, covalent contributions can assume a primary role in the strength and geometry of the complexes. Covalency in chalcogen bonds involves the charge transfer from a lone pair orbital of a Lewis base into the σ* orbital of a divalent chalcogen or a π* orbital of a double bonded chalcogen. We describe for the first time a symmetric chalcogen-bonded homodimer stabilized by a charge transfer from a lone pair orbital into a π* orbital. New polymeric materials based on chalcogen bonds should take advantage of the extra stabilization granted by multiple chalcogen bonds, as is shown for 1,2,5-telluradiazole dimers.
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Affiliation(s)
- Vytor Oliveira
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University , 3215 Daniel Ave, Dallas, Texas 75275-0314, United States
| | - Dieter Cremer
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University , 3215 Daniel Ave, Dallas, Texas 75275-0314, United States
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University , 3215 Daniel Ave, Dallas, Texas 75275-0314, United States
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38
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Echeverría J. Frustrated Lewis Trios and Long-Range Hole Interactions: A Combined Structural and Theoretical Study of LB−AX3
⋅⋅⋅LB and LB⋅⋅⋅AX3
⋅⋅⋅LB (A=B, Al, Ga, In) Systems. Chemphyschem 2017; 18:2864-2872. [DOI: 10.1002/cphc.201700856] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Jorge Echeverría
- Departament de Química Inorgànica i Orgànica and Institut de Química Teòrica i Computacional IQTC-UB; Universitat de Barcelona; Martí i Franquès 1-11 08028 Barcelona Spain
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39
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Wang C, Danovich D, Shaik S, Mo Y. Halogen Bonds in Novel Polyhalogen Monoanions. Chemistry 2017; 23:8719-8728. [DOI: 10.1002/chem.201701116] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Changwei Wang
- College of Science; China University of Petroleum (East China); Changjiangxi Road 66 266580 Tsingtao P. R. China
| | - David Danovich
- Institute of Chemistry and Lise Meitner Minerva Center for Computational Quantum Chemistry; The Hebrew University; Jerusalem 91904 Israel
| | - Sason Shaik
- Institute of Chemistry and Lise Meitner Minerva Center for Computational Quantum Chemistry; The Hebrew University; Jerusalem 91904 Israel
| | - Yirong Mo
- Department of Chemistry; Western Michigan University; Kalamazoo MI 49008 USA
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40
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Geboes Y, De Proft F, Herrebout WA. Effect of Fluorination on the Competition of Halogen Bonding and Hydrogen Bonding: Complexes of Fluoroiodomethane with Dimethyl Ether and Trimethylamine. J Phys Chem A 2017; 121:4180-4188. [PMID: 28493700 DOI: 10.1021/acs.jpca.7b03206] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
To further rationalize the competition between halogen and hydrogen bonding, a combined experimental and theoretical study on the weakly bound molecular complexes formed between the combined halogen bond/hydrogen bond donor fluoroiodomethane and the Lewis bases dimethyl ether and trimethylamine (in standard and fully deuterated form) is presented. The experimental data are obtained by recording infrared and Raman spectra of mixtures of the compounds in liquid krypton, at temperatures between 120 and 156 K. The experiments are supported by ab initio calculations at the MP2/aug-cc-pVDZ-PP level, statistical thermodynamics and Monte Carlo free energy perturbation calculations. For the mixtures containing fluoroiodomethane and dimethyl ether a hydrogen-bonded complex with an experimental complexation enthalpy of -7.0(2) kJ mol-1 is identified. Only a single weak spectral feature is observed which can be tentatively assigned to the halogen-bonded complex. For the mixtures involving trimethylamine, both halogen- and hydrogen-bonded complexes are observed, the experimental complexation enthalpies being -12.5(1) and -9.6(2) kJ mol-1 respectively. To evaluate the influence of fluorination on the competition between halogen and hydrogen bonding, the results obtained for fluoroiodomethane are compared with those of a previous study involving difluoroiodomethane.
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Affiliation(s)
- Yannick Geboes
- Department of Chemistry, University of Antwerp , Groenenborgerlaan 171, 2020 Antwerp, Belgium.,Eenheid Algemene Chemie (ALGC), Member of the QCMM VUB-UGent Alliance Research Group, Vrije Universiteit Brussel (VUB) , Pleinlaan 2, 1050 Brussels, Belgium
| | - Frank De Proft
- Eenheid Algemene Chemie (ALGC), Member of the QCMM VUB-UGent Alliance Research Group, Vrije Universiteit Brussel (VUB) , Pleinlaan 2, 1050 Brussels, Belgium
| | - Wouter A Herrebout
- Department of Chemistry, University of Antwerp , Groenenborgerlaan 171, 2020 Antwerp, Belgium
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41
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Wang C, Danovich D, Shaik S, Mo Y. A Unified Theory for the Blue- and Red-Shifting Phenomena in Hydrogen and Halogen Bonds. J Chem Theory Comput 2017; 13:1626-1637. [DOI: 10.1021/acs.jctc.6b01133] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Changwei Wang
- Department
of Chemistry, School of Science, China University of Petroleum (East China), Changjiangxi Road 66, 266580 Tsingtao, China
| | - David Danovich
- Institute
of Chemistry and Lise Meitner Minerva Center for Computational Quantum
Chemistry, The Hebrew University, Jerusalem 91904, Israel
| | - Sason Shaik
- Institute
of Chemistry and Lise Meitner Minerva Center for Computational Quantum
Chemistry, The Hebrew University, Jerusalem 91904, Israel
| | - Yirong Mo
- Department
of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008, United States
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42
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Preda AM, Schneider WB, Schaarschmidt D, Lang H, Mertens L, Auer AA, Mehring M. The role of dispersion type metal⋯π interaction in the enantiotropic phase transition of two polymorphs of tris-(thienyl)bismuthine. Dalton Trans 2017; 46:13492-13501. [PMID: 28951920 DOI: 10.1039/c7dt02567j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bi(2-C4H3S)3 shows an enantiotropic phase transition that is dominated by London dispersion forces. DFT calculations on model compounds were carried out in order to investigate the competition between Bi⋯S and Bi⋯π heteroarene interaction.
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Affiliation(s)
- A. M. Preda
- Technische Universität Chemnitz
- Fakultät für Naturwissenschaften
- Institut für Chemie
- Professur Koordinationschemie
- 09107 Chemnitz
| | - W. B. Schneider
- Technische Universität Chemnitz
- Fakultät für Naturwissenschaften
- Institut für Chemie
- Professur Koordinationschemie
- 09107 Chemnitz
| | - D. Schaarschmidt
- Technische Universität Chemnitz
- Fakultät für Naturwissenschaften
- Institut für Chemie
- Professur Anorganische Chemie
- 09107 Chemnitz
| | - H. Lang
- Technische Universität Chemnitz
- Fakultät für Naturwissenschaften
- Institut für Chemie
- Professur Anorganische Chemie
- 09107 Chemnitz
| | - L. Mertens
- Technische Universität Chemnitz
- Fakultät für Naturwissenschaften
- Institut für Chemie
- Professur Koordinationschemie
- 09107 Chemnitz
| | - A. A. Auer
- Max-Planck-Institut für Chemische Energiekonversion
- 45470 Mülheim an der Ruhr
- Germany
| | - M. Mehring
- Technische Universität Chemnitz
- Fakultät für Naturwissenschaften
- Institut für Chemie
- Professur Koordinationschemie
- 09107 Chemnitz
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43
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Oliveira V, Kraka E, Cremer D. Quantitative Assessment of Halogen Bonding Utilizing Vibrational Spectroscopy. Inorg Chem 2016; 56:488-502. [PMID: 27966937 DOI: 10.1021/acs.inorgchem.6b02358] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A total of 202 halogen-bonded complexes have been studied using a dual-level approach: ωB97XD/aug-cc-pVTZ was used to determine geometries, natural bond order charges, charge transfer, dipole moments, electron and energy density distributions, vibrational frequencies, local stretching force constants, and relative bond strength orders n. The accuracy of these calculations was checked for a subset of complexes at the CCSD(T)/aug-cc-pVTZ level of theory. Apart from this, all binding energies were verified at the CCSD(T) level. A total of 10 different electronic effects have been identified that contribute to halogen bonding and explain the variation in its intrinsic strength. Strong halogen bonds are found for systems with three-center-four-electron (3c-4e) bonding such as chlorine donors in interaction with substituted phosphines. If halogen bonding is supported by hydrogen bonding, genuine 3c-4e bonding can be realized. Perfluorinated diiodobenzenes form relatively strong halogen bonds with alkylamines as they gain stability due to increased electrostatic interactions.
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Affiliation(s)
- Vytor Oliveira
- Computational and Theoretical Chemistry Group, Department of Chemistry, Southern Methodist University (SMU) , 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group, Department of Chemistry, Southern Methodist University (SMU) , 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Dieter Cremer
- Computational and Theoretical Chemistry Group, Department of Chemistry, Southern Methodist University (SMU) , 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
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44
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Kirshenboim O, Kozuch S. How to Twist, Split and Warp a σ-Hole with Hypervalent Halogens. J Phys Chem A 2016; 120:9431-9445. [PMID: 27783513 DOI: 10.1021/acs.jpca.6b07894] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Halogen bonds (XB) are no longer newcomers in the chemistry family. However, XB in hypervalent halogens has not been thoroughly studied. We provide a molecular orbital explanation of the shape and strength of XBs in hypervalent halogens and other species, focusing on the charge transfer and electrostatic aspects of these bonds. Our results show that σ-holes (and subsequently the XBs associated with them) can be easily divided and bent by the influence of equatorial substituents. The inductive effect of both the equatorial and axial groups can affect these distortions, but also the angle between the equatorial ligands has a large influence on the shape of the σ-holes and the molecular orbitals acting as electron acceptor. Although the observation of these warped XB can be hindered by other noncovalent interactions, they may be ubiquitous in crystal structures of hypervalent species, where multiple XB can appear as secondary interactions on each halogen. We propose what can be considered the archetypal hypervalent halogen donor (a pincer type iodosodilactone) and a Lewis dot structure that includes the σ-holes.
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Affiliation(s)
- Omer Kirshenboim
- Department of Chemistry, Ben-Gurion University of the Negev , Beer-Sheva 841051, Israel
| | - Sebastian Kozuch
- Department of Chemistry, Ben-Gurion University of the Negev , Beer-Sheva 841051, Israel
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45
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Shaw RA, Hill JG, Legon AC. Halogen Bonding with Phosphine: Evidence for Mulliken Inner Complexes and the Importance of Relaxation Energy. J Phys Chem A 2016; 120:8461-8468. [DOI: 10.1021/acs.jpca.6b08945] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Robert A. Shaw
- Department
of Chemistry, University of Sheffield, Sheffield S3 7HF, U.K
| | - J. Grant Hill
- Department
of Chemistry, University of Sheffield, Sheffield S3 7HF, U.K
| | - Anthony C. Legon
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
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46
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Setiawan D, Cremer D. Super-pnicogen bonding in the radical anion of the fluorophosphine dimer. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.09.028] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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47
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48
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Bhasi P, Nhlabatsi ZP, Sitha S. Expanding the applicability of electrostatic potentials to the realm of transition states. Phys Chem Chem Phys 2016; 18:13002-9. [PMID: 27108668 DOI: 10.1039/c6cp01506a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Central to any reaction mechanism study, and sometimes a challenging job, is tracing a transition state in a reaction path. For the first time, electrostatic potentials (ESP) of the reactants were used as guiding tactics to predict whether there is a possibility of any transition state in a reaction surface. The main motive behind this strategy is to see whether the directionality nature of the transition state has something to do with the anisotropic natures of the ESP with their embedded directionalities. Strategically, some atmospherically important, but simple, reactions have been chosen for this study, which heretofore were believed to be barrierless. By carefully analysing the ESP maps of the reactants, regions of possible interactions were located. Using the bilinear interpolation of the 2D grids of the ESP surfaces, search co-ordinates were fine-tuned for a local gradient based approach for the search of a transition state. Out of the three reactions studied in this work, we were able to successfully locate transition states, for the first time, in two cases and the third one still proved to be barrierless. This gives a clear indication that though ESP maps can qualitatively predict the possibility of a transition state; it is not always true that there should definitely be a transition state, as some of the reaction surfaces may genuinely be barrierless. But, nevertheless this strategy definitely has credential to be tested for many more reactions, either new or already established, and may be applied to create the initial search co-ordinates for any well-established transition state search method. Moreover, we have observed that the analysis of the ESP maps of the reactants were very much useful in explaining the nature of interactions existing in those observed transition states and we hope the same can also be extended to any transition state in an electrostatically driven reaction potential energy surface.
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Affiliation(s)
- Priya Bhasi
- Department of Chemistry, University of Johannesburg, PO Box 524, Auckland Park, Johannesburg, 2006, South Africa.
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49
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50
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DiScenza DJ, Levine M. Selective detection of non-aromatic pesticides via cyclodextrin-promoted fluorescence modulation. NEW J CHEM 2016. [DOI: 10.1039/c5nj02357b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The introduction of pesticides to a cyclodextrin-fluorophore solution leads to highly specific fluorescence changes that are used for pesticide detection.
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Affiliation(s)
| | - Mindy Levine
- Department of Chemistry
- University of Rhode Island
- Kingston
- USA
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