1
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Lopresti M, Palin L, Calegari G, Milanesio M. The Peculiar H-Bonding Network of 4-Methylcatechol: A Coupled Diffraction and In Silico Study. Molecules 2024; 29:2173. [PMID: 38792035 PMCID: PMC11124409 DOI: 10.3390/molecules29102173] [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: 03/27/2024] [Revised: 05/02/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024] Open
Abstract
The crystal structure of 4-methylcatechol (4MEC) has, to date, never been solved, despite its very simple chemical formula C7O2H8 and the many possible applications envisaged for this molecule. In this work, this gap is filled and the structure of 4MEC is obtained by combining X-ray powder diffraction and first principle calculations to carefully locate hydrogen atoms. Two molecules are present in the asymmetric unit. Hirshfeld analysis confirmed the reliability of the solved structure, since the two molecules show rather different environments and H-bond interactions of different directionality and strength. The packing is characterised by a peculiar hydrogen bond network with hydroxyl nests formed by two adjacent octagonal frameworks. It is noteworthy that the observed short contacts suggest strong inter-molecular interactions, further confirmed by strong inter-crystalline aggregation observed by microscopic images, indicating the growth, in many crystallization attempts, of single aggregates taller than half a centimetre and, often, with spherical shapes. These peculiarities are induced by the presence of methyl group in 4MEC, since the parent compound catechol, despite its chemical similarity, shows a standard layered packing alternating hydrophobic and polar layers. Finally, the complexity and peculiarity of the packing and crystal growth features explain why a single crystal could not be obtained for a standard structural analysis.
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Affiliation(s)
- Mattia Lopresti
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Viale T. Michel 11, 15121 Alessandria, Italy; (M.L.); (L.P.)
| | - Luca Palin
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Viale T. Michel 11, 15121 Alessandria, Italy; (M.L.); (L.P.)
- Nova Res s.r.l., Via D. Bello 3, 28100 Novara, Italy
| | | | - Marco Milanesio
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Viale T. Michel 11, 15121 Alessandria, Italy; (M.L.); (L.P.)
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2
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Scheiner S. Tetrel Bonding of the Carbenium Ion Forms a Pentacoordinate Carbon Atom. Chemphyschem 2024:e202400240. [PMID: 38527952 DOI: 10.1002/cphc.202400240] [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: 03/04/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 03/27/2024]
Abstract
As a flat trigonal species, the CR3 + carbenium ion contains a pair of deep π-holes above and below its molecular plane. In the case of CH3 + a first base will form a covalent bond with the central C, making the combined species tetrahedral. Approach of a second base to the opposite side results in a longer but rather strong noncovalent tetrel bond (TB). While CMe3 + can also form a similar asymmetric complex with a pair of bases, it also has the capacity to form a pair of nearly equivalent TBs, such that the resulting symmetric trigonal bipyramid configuration is only slightly higher in energy. When the three substituents on the central C are phenyl rings, the symmetric configuration with two TBs predominates. These tetrel bonds are quite strong, reaching up to 20 kcal/mol. Adding OPH2 or OCH substituents to the phenyl rings permits the formation of intramolecular C⋅⋅O TBs to the central C, very similar in many respects to the case where these TBs are intermolecular.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, 84322-0300, Logan, Utah, USA
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3
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Scheiner S, Amonov A. Types of noncovalent bonds within complexes of thiazole with CF 4 and SiF 4. Phys Chem Chem Phys 2024; 26:6127-6137. [PMID: 38299682 DOI: 10.1039/d4cp00057a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
The five-membered heteroaromatic thiazole molecule contains a number of electron-rich regions that could attract an electrophile, namely the N and S lone pairs that lie in the molecular plane, and π-system areas above the plane. The possibility of each of these sites engaging in a tetrel bond (TB) with CF4 and SiF4, as well as geometries that encompass a CH⋯F H-bond, was explored via DFT calculations. There are a number of minima that occur in the pairing of thiazole with CF4 that are very close in energy, but these complexes are weakly bound by less than 2 kcal mol-1 and the presence of a true TB is questionable. The inclusion of zero-point vibrational energies alters the energetic ordering, which is further modified when entropic effects are added. The preferred geometry would thus be sensitive to the temperature of an experiment. Replacement of CF4 by SiF4 leaves intact most of the configurations, and their tight energetic clustering, the ordering of which is again altered as the temperature rises. But there is one exception in that by far the most tightly bound complex involves a strong Si⋯N TB between SiF4 and the lone pair of the thiazole N, with an interaction energy of 30 kcal mol-1. Even accounting for its high deformation energy and entropic considerations, this structure remains as clearly the most stable at any temperature.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry Utah State University Logan, Utah 84322-0300, USA.
| | - Akhtam Amonov
- Department of Optics and Spectroscopy, Institute of Engineering Physics Samarkand State University 140104, University blv. 15, Samarkand, Uzbekistan
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4
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Michalczyk M, Zierkiewicz W, Scheiner S. Wolfium bonds in homodimers of MX 4Y (M = Mo, W; X = F, Cl, Br; Y = O, S, Se). Phys Chem Chem Phys 2024; 26:5836-5847. [PMID: 38299423 DOI: 10.1039/d3cp05867k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
The term "wolfium bond" has been recently introduced to describe the noncovalent attraction between an atom of group 6 and a nucleophile via a σ-hole binding site. Crystal structures commonly contain a motif wherein two MX4Y units are arranged in close proximity, where M represents either Mo or W, and X and Y refer to halogen and chalcogen atoms respectively. DFT calculations were thus applied to a wide range of homodimers of these molecules so as to assess their preferred arrangements, and to characterize the types of bonding that are present in each in a systematic manner. The most stable Dual-X configuration is symmetric and contains a pair of equivalent M⋯X bonds. The interaction energies range from -8 to -29 kcal mol-1, and are largest for X = F, Y = O, and M = W. The X electron donor is replaced by Y, and the two wolfium bonds are reduced to one, in the less stable Mono-Y structure, with interaction energies between -2 and -10 kcal mol-1. There is some question as to whether the weaker bonds of this type constitute true wolfium bonds.
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Affiliation(s)
- Mariusz Michalczyk
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Wiktor Zierkiewicz
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University Logan, Utah 84322-0300, USA
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5
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Dasgupta S, Palos E, Pan Y, Paesani F. Balance between Physical Interpretability and Energetic Predictability in Widely Used Dispersion-Corrected Density Functionals. J Chem Theory Comput 2024; 20:49-67. [PMID: 38150541 DOI: 10.1021/acs.jctc.3c00903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
We assess the performance of different dispersion models for several popular density functionals across a diverse set of noncovalent systems, ranging from the benzene dimer to molecular crystals. By analyzing the interaction energies and their individual components, we demonstrate that there exists variability across different systems for empirical dispersion models, which are calibrated for reproducing the interaction energies of specific systems. Thus, parameter fitting may undermine the underlying physics, as dispersion models rely on error compensation among the different components of the interaction energy. Energy decomposition analyses reveal that, the accuracy of revPBE-D3 for some aqueous systems originates from significant compensation between dispersion and charge transfer energies. However, revPBE-D3 is less accurate in describing systems where error compensation is incomplete, such as the benzene dimer. Such cases highlight the propensity for unpredictable behavior in various dispersion-corrected density functionals across a wide range of molecular systems, akin to the behavior of force fields. On the other hand, we find that SCAN-rVV10, a targeted-dispersion approach, affords significant reductions in errors associated with the lattice energies of molecular crystals, while it has limited accuracy in reproducing structural properties. Given the ubiquitous nature of noncovalent interactions and the key role of density functional theory in computational sciences, the future development of dispersion models should prioritize the faithful description of the dispersion energy, a shift that promises greater accuracy in capturing the underlying physics across diverse molecular and extended systems.
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Affiliation(s)
- Saswata Dasgupta
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Etienne Palos
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Yuanhui Pan
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
- Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, United States
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
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6
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Scheiner S, Michalczyk M, Zierkiewicz W. Influence of Internal Angular Arrangement on Pnicogen Bond Strength. Inorg Chem 2023. [PMID: 38016913 DOI: 10.1021/acs.inorgchem.3c03141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
The three Z-X covalent bonds of a ZX3 unit (Z = P, As, Sb, Bi) are normally arranged in a pyramidal structure. Quantum chemical calculations show that pnicogen bonds (ZBs) to the central Z are weakened if ZX3 is flattened, as in the opening of an umbrella. The partial closing of the umbrella has the opposite effect of substantially strengthening these ZBs, even amounting to a 2- or 3-fold magnification in certain cases. The strongest such bonds, wherein Sb and Bi are in a strained configuration within a ZO3CH model system, have interaction energies of 20 kcal/mol with an NH3 base. Most of these systems, whether flattened or more pyramidal, are capable of engaging in three ZBs simultaneously, despite a certain amount of negative cooperativity.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
| | - Mariusz Michalczyk
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Wiktor Zierkiewicz
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
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7
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Scheiner S. Transition between the Noncovalency and Covalency of σ-Hole Bonds. J Phys Chem A 2023; 127:9760-9770. [PMID: 37943718 DOI: 10.1021/acs.jpca.3c06093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
The properties of the bond between a N-ligand and a Lewis acid containing a σ-hole are studied by quantum chemical methods. Interactions considered include pnicogen bonds involving SbX5, PX5, and PX3, where X represents any of the halogen atoms F, Cl, Br, or I. Also studied are the tetrel bonds of PbX4 and SiX4, as well as the chalcogen bond involving TeOX4. Both NH3 and NCH are applied as two possible bases of differing potency. Some of the bonds are very strong with interaction energies easily exceeding 25 kcal/mol and with AIM bond critical point densities much higher than 0.04 au, suggesting their classification as coordinate covalent bonds. The pentavalent SbX5 and PX5 fall into this category when combined with NH3, as does TeOX4. Although the tetrel bonds involving PbX4 are only slightly weaker, they are probably better viewed as a strong noncovalent bond on the cusp of covalency. Changing the internal bonding of hypervalent SbX5 to the more conventional SbX3 weakens the interaction to a classical noncovalent pnicogen bond. Reducing the base nucleophilicity from NH3 to NCH weakens the bonds so that they are clearly noncovalent.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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8
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Briccolani-Bandini L, Brémond E, Pagliai M, Cardini G, Ciofini I, Adamo C. Concerted versus stepwise proton transfer reactions in the [2, 2'-bipyridyl]-3-3'-diol molecule: A static and dynamic ab-initio investigation. J Comput Chem 2023; 44:2308-2318. [PMID: 37584183 DOI: 10.1002/jcc.27198] [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: 04/11/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 08/17/2023]
Abstract
The double proton transfer (PT) reaction has been investigated in the [2,2'-bipyridyl]-3-3'-diol, a complex molecule where the proton movements is coupled to significant rearrangement of the electronic structure. Moreover, the reaction could be concerted, that is the two protons are exchanged simultaneously, or stepwise, where the two protons are transferred sequentially. To this end, a static exploration of the potential energy surface (PES) was carried together with the analysis of the free-energy surface (FES), both surfaces being evaluated at density functional theory level and different exchange-correlation functionals. While the concerted mechanism has been clearly discharged, the characteristics of the stepwise PT significantly depends on the chosen functionals, some suggesting a clear stepwise mechanism characterized by a stable reaction intermediates and two transitions states, whereas other approaches propend for a asynchronous PT, with a single TS. These features appear on both PES and FES, albeit some differences appears due to their different nature.
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Affiliation(s)
| | - Eric Brémond
- ITODYS, CNRS, Université Paris Cité, Paris, France
| | - Marco Pagliai
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Sesto Fiorentino, Italy
| | - Gianni Cardini
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Sesto Fiorentino, Italy
| | - Ilaria Ciofini
- CNRS, i-CLeHS, UMR 8060, Chimie ParisTech, PSL University, Paris, France
| | - Carlo Adamo
- CNRS, i-CLeHS, UMR 8060, Chimie ParisTech, PSL University, Paris, France
- Institut Universitaire de France, Paris, France
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9
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Amonov A, Scheiner S. Relation between Halogen Bond Strength and IR and NMR Spectroscopic Markers. Molecules 2023; 28:7520. [PMID: 38005241 PMCID: PMC10673387 DOI: 10.3390/molecules28227520] [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: 10/23/2023] [Revised: 11/04/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
The relationship between the strength of a halogen bond (XB) and various IR and NMR spectroscopic quantities is assessed through DFT calculations. Three different Lewis acids place a Br or I atom on a phenyl ring; each is paired with a collection of N and O bases of varying electron donor power. The weakest of the XBs display a C-X bond contraction coupled with a blue shift in the associated frequency, whereas the reverse trends occur for the stronger bonds. The best correlations with the XB interaction energy are observed with the NMR shielding of the C atom directly bonded to X and the coupling constants involving the C-X bond and the C-H/F bond that lies ortho to the X substituent, but these correlations are not accurate enough for the quantitative assessment of energy. These correlations tend to improve as the Lewis acid becomes more potent, which makes for a wider range of XB strengths.
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Affiliation(s)
- Akhtam Amonov
- Department of Optics and Spectroscopy, Engineering Physics Institute, Samarkand State University, University blv. 15, Samarkand 140104, Uzbekistan;
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA
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10
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Ovchinnikov MY, Kuzmina EV, Karaseva EV, Khursan SL, Kolosnitsyn VS. DFT Model of Elemental Sulfur in Sulfolane Solutions. J Phys Chem A 2023; 127:8971-8984. [PMID: 37862674 DOI: 10.1021/acs.jpca.3c04104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
Abstract
The structure and the thermodynamic and optical (UV) properties of elemental sulfur solution in sulfolane (Sl) have been studied using density functional theory methods. The cyclic molecular form of sulfur (S8 "crown") was found using PBE1PBE/6-311+G(d,p) approximation in combination with a polarizable continuum model (the integral equation formalism variant) to exist in sulfolane medium as a Sl-S8-Sl solvate. It has been theoretically established that sulfur can form stable (S8)n clusters in concentrated solutions. An increase in the extent of association (n) of the sulfur cluster leads to a decrease in the extinction coefficient [TD-DFT(TPSSTPSS/6-311+G(d,p))] of the most intense absorption maximum lying at about 50,000 cm-1 while maintaining the shape of the remaining part of the spectrum. The observed pattern qualitatively expresses the spectral regularities of solutions with different concentrations of sulfur in sulfolane. It has been proposed that a model of the absorption spectrum of elemental sulfur suggests a minor contribution of the S12 molecular form (G298°((S12)2) - G298°((S8)3) ≈ -15.5 kJ mol-1). The findings of the study will provide deeper insights into the transformation of molecular forms of sulfur and more precisely analyze processes involving sulfur as an acting species using electronic spectroscopy.
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11
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Le T, Wang B. Solvent-induced local environment effect in plasmonic catalysis. NANOSCALE ADVANCES 2023; 5:5774-5779. [PMID: 37881713 PMCID: PMC10597543 DOI: 10.1039/d3na00835e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 09/30/2023] [Indexed: 10/27/2023]
Abstract
Solvents are known to affect the local surface plasmon resonance of metal nanoparticles; however, how solvents can be used to manipulate the interfacial charge and energy transfer in plasmonic catalysis remains to be explored. Here, using NH3 decomposition on a Ru-doped Cu surface as an example, we report density functional theory (DFT) and delta self-consistent field (SCF) calculations, through which we investigate the effect of different protic solvent molecules on interfacial charge transfer by calculating excitation energy of an electronic transition between the metal and the molecular reactant. We find that the H-bonds between water and NH3 can alter the direct interfacial charge transfer due to the shift of the molecular frontier orbitals with respect to the metal Fermi level. These effects are also observed when the H-bonds are formed between methanol (or phenol) and ammonia. We show that the solvent possessing stronger basicity induces a more pronounced effect on the excitation energy. This work thus provides valuable insights for tuning the excitation energy and controlling different routes to channel the photon energy into plasmonic catalysis.
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Affiliation(s)
- Tien Le
- School of Sustainable Chemical, Biological and Materials Engineering, University of Oklahoma Norman OK 73019 USA
| | - Bin Wang
- School of Sustainable Chemical, Biological and Materials Engineering, University of Oklahoma Norman OK 73019 USA
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12
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Amonov A, Scheiner S. Heavy pnicogen atoms as electron donors in sigma-hole bonds. Phys Chem Chem Phys 2023; 25:23530-23537. [PMID: 37656119 DOI: 10.1039/d3cp03479h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
DFT calculations evaluate the strength of σ-hole bonds formed by ZH3 and ZMe3 (Z = N, P, As, Sb) acting as electron donor. Bond types considered include H-bond, halogen, chalcogen, pnicogen, and tetrel bond to perfluorinated Lewis acids FH, FBr, F2Se F3As, F4Ge, respectively, as well as their monofluorinated analogues. All of the Z atoms can engage in bonds of at least moderate strength, varying from 3 to more than 40 kcal mol-1. In most cases, N forms the strongest bonds, but the falloff from P to Sb is quite mild. However, this pattern is not characteristic of all cases, as for example in the halogen bonds, where the heavier Z atoms are comparable to, or even stronger than N. Most of the bonds are strengthened by replacing the three H atoms of ZH3 by methyl groups, better simulating the situation that would be generally encountered. Structural and NMR shielding data ought to facilitate the identification of these bonds within crystals or in solution.
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Affiliation(s)
- Akhtam Amonov
- Department of Optics and Spectroscopy Engineering Physics Institute, Samarkand State University, University blv. 15, Samarkand 140104, Uzbekistan
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University Logan, Utah 84322-0300, USA.
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13
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Amonov A, Scheiner S. Competition between Binding to Various Sites of Substituted Imidazoliums. J Phys Chem A 2023. [PMID: 37490696 DOI: 10.1021/acs.jpca.3c04097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
The imidazolium cation has a number of different sites that can interact with a nucleophile. Adding a halogen atom (X) or a chalcogen (YH) group introduces the possibility of an NX···nuc halogen or NY···nuc chalcogen bond, which competes against the various H-bonds (NH and CH donors) as well as the lone pair···π interaction wherein the nucleophile lies above the plane of the cation. Substituted imidazoliums are paired with the NH3 base, and the various different complexes are evaluated by density functional theory (DFT) calculations. The strength of XB and YB increases quickly along with the size and polarizability of the X/Y atom, and this sort of bond is the strongest for the heavier Br, I, Se, and Te atoms, followed by the NH···N H-bond, but this order reverses for Cl and S. The various CH···N H-bonds are comparable to one another and to the lone pair···π bond, all with interaction energies of 10-13 kcal/mol, values which show very little dependence upon the substituent placed on the imidazolium.
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Affiliation(s)
- Akhtam Amonov
- Department of Optics and Spectroscopy, Engineering Physics Institute, Samarkand State University, University blv. 15, Samarkand 140104, Uzbekistan
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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14
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Xie R, Hu Y, Lee SL. A Paradigm Shift from 2D to 3D: Surface Supramolecular Assemblies and Their Electronic Properties Explored by Scanning Tunneling Microscopy and Spectroscopy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2300413. [PMID: 36922729 DOI: 10.1002/smll.202300413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/21/2023] [Indexed: 06/15/2023]
Abstract
Exploring supramolecular architectures at surfaces plays an increasingly important role in contemporary science, especially for molecular electronics. A paradigm of research interest in this context is shifting from 2D to 3D that is expanding from monolayer, bilayers, to multilayers. Taking advantage of its high-resolution insight into monolayers and a few layers, scanning tunneling microscopy/spectroscopy (STM/STS) turns out a powerful tool for analyzing such thin films on a solid surface. This review summarizes the representative efforts of STM/STS studies of layered supramolecular assemblies and their unique electronic properties, especially at the liquid-solid interface. The superiority of the 3D molecular networks at surfaces is elucidated and an outlook on the challenges that still lie ahead is provided. This review not only highlights the profound progress in 3D supramolecular assemblies but also provides researchers with unusual concepts to design surface supramolecular structures with increasing complexity and desired functionality.
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Affiliation(s)
- Rongbin Xie
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
- College of Civil and Transportation Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Yi Hu
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Shern-Long Lee
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
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15
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Abstract
Quantum calculations study the potential of an intramolecular H-bond between the halogen atom (X) of a halobenzene and a substituent placed ortho to it, to amplify the ability of X to engage in a halogen bond (XB) with a Lewis base. H-bonding substituents NH2, CH2CH2OH, CH2OH, OH, and COOH were added to halobenzenes (X = Cl, Br, I). The amino group had little effect, but those containing OH increased the CX···N XB energy to a NH3 nucleophile by about 0.5 kcal/mol; the increment associated with COOH is larger, nearly 2 kcal/mol. These energy increments were approximately doubled if two such H-bonding substituents are present. Combining a pair of ortho COOH groups with an electron-withdrawing NO2 group in the para position has a particularly large effect, raising the XB energy by about 4 kcal/mol, which can amount to as much as a 4-fold magnification.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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16
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Maletta A, Gutiérrez A, Jian Tan P, Springstead J, Aparicio S, Atilhan M. Separation of Phenolic Compounds from Water by using Monoterpenoid and Fatty Acid Based Hydrophobic Deep Eutectic Solvents. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
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17
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Picci G, Aragoni MC, Arca M, Caltagirone C, Formica M, Fusi V, Giorgi L, Ingargiola F, Lippolis V, Macedi E, Mancini L, Mummolo L, Prodi L. Fluorescent sensing of non-steroidal anti-inflammatory drugs naproxen and ketoprofen by dansylated squaramide-based receptors. Org Biomol Chem 2023; 21:2968-2975. [PMID: 36938589 DOI: 10.1039/d3ob00324h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Bis-squaramide receptors L1-L4 bearing a dansyl moiety were synthesised and their potential applications as fluorescent probes towards non steroidal anti-inflammatory drugs naproxen and ketoprofen was investigated. A detailed photophysical characterization in CH3CN/DMSO solution (9 : 1 v/v) was conducted and demonstrated that the two macrocyclic receptors L1 and L2 show good sensitivity towards ketoprofen with an ON-OFF fluorescent response, while the two open chain receptors L3 and L4 behave similarly with the three guests considered. DFT theoretical calculations carried out on L2 and L4 as model receptors allowed to propose a possible coordination mode towards the guests. Finally, 1H-NMR spectroscopy in DMSO-d6/0.5% water solution demonstrated that the four receptors interact with the considered guests via H-bonds.
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Affiliation(s)
- Giacomo Picci
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 Bivio per Sestu, 09042 Monserrato, CA, Italy.
| | - M Carla Aragoni
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 Bivio per Sestu, 09042 Monserrato, CA, Italy.
| | - Massimiliano Arca
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 Bivio per Sestu, 09042 Monserrato, CA, Italy.
| | - Claudia Caltagirone
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 Bivio per Sestu, 09042 Monserrato, CA, Italy.
| | - Mauro Formica
- Department of Pure and Applied Science, University of Urbino, Via della Stazione 4, I-61029 Urbino, Italy.
| | - Vieri Fusi
- Department of Pure and Applied Science, University of Urbino, Via della Stazione 4, I-61029 Urbino, Italy.
| | - Luca Giorgi
- Department of Pure and Applied Science, University of Urbino, Via della Stazione 4, I-61029 Urbino, Italy.
| | - Filippo Ingargiola
- Department of Chemistry "Giacomo Ciamician", Università degli Studi di Bologna, Via Selmi 2, 40126 Bologna, Italy.
| | - Vito Lippolis
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 Bivio per Sestu, 09042 Monserrato, CA, Italy.
| | - Eleonora Macedi
- Department of Pure and Applied Science, University of Urbino, Via della Stazione 4, I-61029 Urbino, Italy.
| | - Luca Mancini
- Department of Pure and Applied Science, University of Urbino, Via della Stazione 4, I-61029 Urbino, Italy.
| | - Liviana Mummolo
- Department of Chemistry "Giacomo Ciamician", Università degli Studi di Bologna, Via Selmi 2, 40126 Bologna, Italy.
| | - Luca Prodi
- Department of Chemistry "Giacomo Ciamician", Università degli Studi di Bologna, Via Selmi 2, 40126 Bologna, Italy.
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18
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Scheiner S. Does a halogen bond require positive potential on the acid and negative potential on the base? Phys Chem Chem Phys 2023; 25:7184-7194. [PMID: 36815530 DOI: 10.1039/d3cp00379e] [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
It is usually expected that formation of a halogen bond (XB) requires that a region of positive electrostatic potential associated with a σ or π-hole on the Lewis acid will interact with the negative potential of the base, either a lone pair or π-bond region. Quantum calculations of model systems suggest this not to be necessary. The placement of electron-withdrawing substituents on the base can reverse the sign of the potential in its lone pair or π-bond region to positive, and this base can nonetheless engage in a XB with the positive σ-hole of a Lewis acid. The reverse scenario is also possible in certain circumstances, as a negatively charged σ-hole can form a XB with the negative lone pair region of a base. Despite these classical Coulombic repulsions, the overall electrostatic interaction is attractive in these XBs, albeit only weakly so. The strengths of these bonds are surprisingly insensitive to changes in the partner molecule. For example, even a wide range in the depth of the σ-hole of the approaching acid yields only a minimal change in the strength of the XB to a base with a positive potential.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry Utah State University Logan, Utah, USA, 84322-0300.
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19
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Hoelm M, Adamczyk J, Wzgarda-Raj K, Palusiak M. Effect of a Substituent on the Properties of Salicylaldehyde Hydrazone Derivatives. J Org Chem 2023; 88:2132-2139. [PMID: 36735741 PMCID: PMC9942203 DOI: 10.1021/acs.joc.2c02547] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The present study investigates the effect of the substitution of salicylaldehyde hydrazones at two selected positions, i.e., the para-position with regard to the proton-donating and proton-accepting centers forming the hydrogen bridge. A detailed analysis of structural data obtained by theoretical approaches and X-ray experiments, together with original resonance Hammett's constants, indicates that the strength of the intramolecular hydrogen bonding present in salicylaldehyde hydrazones can be selectively modulated by substitution of the parent molecular system with the chemical group of known π-electron-donating or -accepting properties. Our findings provide an insight into planning synthesis pathways for salicylaldehyde hydrazone species and predicting their result with regard to their H-bonding and related physical and chemical properties.
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Affiliation(s)
- Marta Hoelm
- Department
of Physical Chemistry, Faculty of Chemistry, University of Lodz, Pomorska 163/165, Lodz90-236, Poland
| | - Justyna Adamczyk
- Department
of Organic and Applied Chemistry, Faculty of Chemistry, University of Lodz, Tamka 12, Lodz91-403, Poland
| | - Kinga Wzgarda-Raj
- Department
of Physical Chemistry, Faculty of Chemistry, University of Lodz, Pomorska 163/165, Lodz90-236, Poland
| | - Marcin Palusiak
- Department
of Physical Chemistry, Faculty of Chemistry, University of Lodz, Pomorska 163/165, Lodz90-236, Poland,
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20
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Valenti S, Cazorla C, Romanini M, Tamarit JL, Macovez R. Eutectic Mixture Formation and Relaxation Dynamics of Coamorphous Mixtures of Two Benzodiazepine Drugs. Pharmaceutics 2023; 15:pharmaceutics15010196. [PMID: 36678825 PMCID: PMC9861849 DOI: 10.3390/pharmaceutics15010196] [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: 12/02/2022] [Revised: 12/27/2022] [Accepted: 12/30/2022] [Indexed: 01/09/2023] Open
Abstract
The formation of coamorphous mixtures of pharmaceuticals is an interesting strategy to improve the solubility and bioavailability of drugs, while at the same time enhancing the kinetic stability of the resulting binary glass and allowing the simultaneous administration of two active principles. In this contribution, we describe kinetically stable amorphous binary mixtures of two commercial active pharmaceutical ingredients, diazepam and nordazepam, of which the latter, besides being administered as a drug on its own, is also the main active metabolite of the other in the human body. We report the eutectic equilibrium-phase diagram of the binary mixture, which is found to be characterized by an experimental eutectic composition of 0.18 molar fraction of nordazepam, with a eutectic melting point of Te = 395.4 ± 1.2 K. The two compounds are barely miscible in the crystalline phase. The mechanically obtained mixtures were melted and supercooled to study the glass-transition and molecular-relaxation dynamics of amorphous mixtures at the corresponding concentration. The glass-transition temperature was always higher than room temperature and varied linearly with composition. The Te was lower than the onset of thermal decomposition of either compound (pure nordazepam decomposes upon melting and pure diazepam well above its melting point), thus implying that the eutectic liquid and glass can be obtained without any degradation of the drugs. The eutectic glass was kinetically stable against crystallization for at least a few months. The relaxation processes of the amorphous mixtures were studied by dielectric spectroscopy, which provided evidence for a single structural (α) relaxation, a single Johari-Goldstein (β) relaxation, and a ring-inversion conformational relaxation of the diazepinic ring, occurring on the same timescale in both drugs. We further characterized both the binary mixtures and pure compounds by FTIR spectroscopy and first-principles density functional theory (DFT) simulations to analyze intermolecular interactions. The DFT calculations confirm the presence of strong attractive forces within the heteromolecular dimer, leading to large dimer interaction energies of the order of -0.1 eV.
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21
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Scheiner S. Adjusting the balance between hydrogen and chalcogen bonds. Phys Chem Chem Phys 2022; 24:28944-28955. [PMID: 36416473 DOI: 10.1039/d2cp04591e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A complex is assembled which pairs a carboxyl group of X1COOH with a 1,2,5-chalcogenadiazole ring containing substituents on its C atoms. The OH of the carboxyl group donates a proton to a N atom of the ring to form a OH⋯N H-bond (HB), while its carbonyl O engages in a Y⋯O chalcogen bond (ChB) with the ring in which Y = S, Se, Te. The ChB is strengthened by enlarging the size of the Y atom from S to Se to Te. Placement of an electron-withdrawing group (EWG) X1 on the acid strengthens the HB while weakening the ChB; the reverse occurs when EWGs are placed on the ring. By selection of the proper substituents on the two units, it is possible to achieve a near perfect balance between the strengths of these two bonds. These bond strengths are also reflected in the NMR spectroscopic properties of the chemical shielding of the various atoms and the coupling between the nuclei directly involved in each bond.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA.
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22
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Domagała M, Jabłoński M, Dubis AT, Zabel M, Pfitzner A, Palusiak M. Testing of Exchange-Correlation Functionals of DFT for a Reliable Description of the Electron Density Distribution in Organic Molecules. Int J Mol Sci 2022; 23:ijms232314719. [PMID: 36499046 PMCID: PMC9740346 DOI: 10.3390/ijms232314719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/08/2022] [Accepted: 11/18/2022] [Indexed: 11/27/2022] Open
Abstract
Researchers carrying out calculations using the DFT method face the problem of the correct choice of the exchange-correlation functional to describe the quantities they are interested in. This article deals with benchmark calculations aimed at testing various exchange-correlation functionals in terms of a reliable description of the electron density distribution in molecules. For this purpose, 30 functionals representing all rungs of Jacob's Ladder are selected and then the values of some QTAIM-based parameters are compared with their reference equivalents obtained at the CCSD/aug-cc-pVTZ level of theory. The presented results show that the DFT method undoubtedly has the greatest problems with a reliable description of the electron density distribution in multiple strongly polar bonds, such as C=O, and bonds associated with large electron charge delocalization. The performance of the tested functionals turned out to be unsystematic. Nevertheless, in terms of a reliable general description of QTAIM-based parameters, the M11, SVWN, BHHLYP, M06-HF, and, to a slightly lesser extent, also BLYP, B3LYP, and X3LYP functionals turned out to be the worst. It is alarming to find the most popular B3LYP functional in this group. On the other hand, in the case of the electron density at the bond critical point, being the most important QTAIM-based parameter, the M06-HF functional is especially discouraged due to the very poor description of the C=O bond. On the contrary, the VSXC, M06-L, SOGGA11-X, M06-2X, MN12-SX, and, to a slightly lesser extent, also TPSS, TPSSh, and B1B95 perform well in this respect. Particularly noteworthy is the overwhelming performance of double hybrids in terms of reliable values of bond delocalization indices. The results show that there is no clear improvement in the reliability of describing the electron density distribution with climbing Jacob's Ladder, as top-ranked double hybrids are also, in some cases, able to produce poor values compared to CCSD.
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Affiliation(s)
- Małgorzata Domagała
- Faculty of Chemistry, University of Lodz, Pomorska 163/165, 90-236 Lodz, Poland
| | - Mirosław Jabłoński
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100 Toruń, Poland
- Correspondence: ; Tel.: +48-056-611-4695
| | - Alina T. Dubis
- Faculty of Chemistry, University of Białystok, Ciołkowskiego 1K, 15-245 Białystok, Poland
| | - Manfred Zabel
- Institute of Inorganic Chemistry, University of Regensburg, Universitätsstr. 31, 93040 Regensburg, Germany
| | - Arno Pfitzner
- Institute of Inorganic Chemistry, University of Regensburg, Universitätsstr. 31, 93040 Regensburg, Germany
| | - Marcin Palusiak
- Faculty of Chemistry, University of Lodz, Pomorska 163/165, 90-236 Lodz, Poland
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23
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Pokorný V, Touš P, Štejfa V, Růžička K, Rohlíček J, Czernek J, Brus J, Červinka C. Anisotropy, segmental dynamics and polymorphism of crystalline biogenic carboxylic acids. Phys Chem Chem Phys 2022; 24:25904-25917. [PMID: 36260017 DOI: 10.1039/d2cp03698c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Carboxylic acids of the Krebs cycle possess invaluable biochemical significance. Still, there are severe gaps in the availability of thermodynamic and crystallographic data, as well as ambiguities prevailing in the literature on the thermodynamic characterization and polymorph ranking. Providing an unambiguous description of the structure, thermodynamics and polymorphism of their neat crystalline phases requires a complex multidisciplinary approach. This work presents results of an extensive investigation of the structural anisotropy of the thermal expansion and local dynamics within these crystals, obtained from a beneficial cooperation of NMR crystallography and ab initio calculations of non-covalent interactions. The observed structural anisotropy and spin-lattice relaxation times are traced to large spatial variations in the strength of molecular interactions in the crystal lattice, especially in the orientation of the hydrogen bonds. A completely resolved crystal structure for oxaloacetic acid is reported for the first time. Thanks to multi-instrumental calorimetric effort, this work clarifies phase behavior, determines third-law entropies of the crystals, and states definitive polymorph ranking for succinic and fumaric acids. These thermodynamic observations are then interpreted in terms of first-principles quasi-harmonic calculations of cohesive properties. A sophisticated model capturing electronic, thermal, and configurational-entropic effects on the crystal structure approaches captures the subtle Gibbs energy differences governing polymorph ranking for succinic and fumaric acids, representing another success story of computational chemistry.
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Affiliation(s)
- Václav Pokorný
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic.
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského nám. 2, CZ-162 06 Prague 6, Czech Republic
| | - Petr Touš
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic.
| | - Vojtěch Štejfa
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic.
| | - Květoslav Růžička
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic.
| | - Jan Rohlíček
- Institute of Physics, Czech Academy of Sciences, Na Slovance 2, CZ-182 21 Prague 8, Czech Republic
| | - Jiří Czernek
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského nám. 2, CZ-162 06 Prague 6, Czech Republic
| | - Jiří Brus
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského nám. 2, CZ-162 06 Prague 6, Czech Republic
| | - Ctirad Červinka
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic.
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24
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Scheiner S. Properties and Stabilities of Cyclic and Open Chains of Halogen Bonds. J Phys Chem A 2022; 126:6443-6455. [PMID: 36084144 DOI: 10.1021/acs.jpca.2c04967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Open and cyclic chains from two to eight units of ICl and IF are constructed and examined by density functional theory (DFT) calculations. These chains contain either I···I or I···X halogen bonds (XBs) where X refers to Cl or F. The closed rings are more stable than the open chains due to the presence of an additional XB and enhanced cooperativity. This pattern is true even for most trimers where there is sizable geometric distortion in the rings. I···F rings are generally more stable than the corresponding I···I cycles as the I···F bond is stronger than I···I even in the simple dimer. However, I···I rings are comparable in energy to I···Cl. It is possible to construct I···I rings of at least as large as eight units, which are held together exclusively by XBs. On the other hand, the maximum possible size of I···X rings is 6. Red shifts are observed in the I-X stretching frequency bands, which magnify as the chain, both cyclic and open, grows longer. The NMR chemical shielding of the I atoms increases for I···I chains but diminishes when I···Cl bonds are present.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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25
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Sparrow ZM, Ernst BG, Quady TK, DiStasio RA. Uniting Nonempirical and Empirical Density Functional Approximation Strategies Using Constraint-Based Regularization. J Phys Chem Lett 2022; 13:6896-6904. [PMID: 35863751 DOI: 10.1021/acs.jpclett.2c00643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In this work, we present a general framework that unites the two primary strategies for constructing density functional approximations (DFAs): nonempirical (NE) constraint satisfaction and empirical (E) data-driven optimization. The proposed method employs B-splines, bell-shaped spline functions with compact support, to construct each inhomogeneity correction factor (ICF). This choice offers several distinct advantages over traditional polynomial expansions by enabling explicit enforcement of linear and nonlinear constraints as well as ICF smoothness using Tikhonov and penalized B-splines (P-splines) regularization. As proof-of-concept, we use the so-called CASE (constrained and smoothed empirical) framework to construct a constraint-satisfying and data-driven global hybrid that exhibits enhanced performance across a diverse set of chemical properties. We argue that the CASE approach can be used to generate DFAs that maintain the physical rigor and transferability of NE-DFAs while leveraging high-quality quantum-mechanical data to remove the arbitrariness of ansatz selection and improve performance.
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Affiliation(s)
- Zachary M Sparrow
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Brian G Ernst
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Trine K Quady
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Robert A DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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26
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Nandy A, Adamji H, Kastner DW, Vennelakanti V, Nazemi A, Liu M, Kulik HJ. Using Computational Chemistry To Reveal Nature’s Blueprints for Single-Site Catalysis of C–H Activation. ACS Catal 2022. [DOI: 10.1021/acscatal.2c02096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Aditya Nandy
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Husain Adamji
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - David W. Kastner
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Vyshnavi Vennelakanti
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Azadeh Nazemi
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mingjie Liu
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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27
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Empel C, Pei C, He F, Jana S, Koenigs RM. Proton or Carbene Transfer? On the Dark and Light Reaction of Diazoalkanes with Alcohols. Chemistry 2022; 28:e202104397. [PMID: 35060651 PMCID: PMC9306865 DOI: 10.1002/chem.202104397] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Indexed: 12/23/2022]
Abstract
The formal alkylation reaction of OH groups with diazoalkanes under catalyst-free reaction conditions finds broad application in organic synthesis. However, even today, this reaction is mainly limited to the use of diazomethane as reaction partner. In this combined experimental and theoretical study, we aim at a fundamental understanding of the reaction of diazoalkanes with alcohols to make this transformation amenable to a generalized approach towards formal alkylation reactions of alcohols with diazoalkanes. Experimental and theoretical studies suggest a direct proton transfer only in exceptional cases. In a more general setting, such O-H functionalization proceed both under dark and photochemical conditions via a key hydrogen-bonded singlet carbene intermediate that undergoes a protonation-addition mechanism. We conclude with applications of this approach in O-H functionalization reactions of alcohols, including simple fluorinated, halogenated and aliphatic alcohols and showcase functional-group tolerance of this method in the reaction of biologically active and pharmaceutically relevant alcohols.
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Affiliation(s)
- Claire Empel
- RWTH Aachen University, Institute of Organic Chemistry, Landoltweg 1, D-52074, Aachen, Germany
| | - Chao Pei
- RWTH Aachen University, Institute of Organic Chemistry, Landoltweg 1, D-52074, Aachen, Germany
| | - Feifei He
- RWTH Aachen University, Institute of Organic Chemistry, Landoltweg 1, D-52074, Aachen, Germany
| | - Sripati Jana
- RWTH Aachen University, Institute of Organic Chemistry, Landoltweg 1, D-52074, Aachen, Germany
| | - Rene M Koenigs
- RWTH Aachen University, Institute of Organic Chemistry, Landoltweg 1, D-52074, Aachen, Germany
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28
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Kohlmann T, Goez M. The radicals of quercetin-derived antioxidants in Triton X-100 micelles. Phys Chem Chem Phys 2022; 24:5868-5878. [DOI: 10.1039/d1cp04690j] [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
We have employed photoionization with a pulsed laser (5 ns, 355 nm) as a direct access to the radicals of quercetin, five of its monoethers and three of its diethers...
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29
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Ignaczak A, Orszański Ł. In Search of the Most Stable Molecular Configuration of Heptakis(2,6- O-dimethyl)-β-cyclodextrin and Its Complex with Mianserin: A Comparison of the B3LYP-GD2 and M062X-GD3 Results. J Phys Chem B 2021; 125:13077-13087. [PMID: 34817179 PMCID: PMC8667041 DOI: 10.1021/acs.jpcb.1c06831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cyclodextrins are well known for their ability to form stable, highly soluble complexes with various substances, which makes them widely used as excipients in food, cosmetics, and pharmaceuticals. In this work, properties of heptakis(2,6-O-dimethyl)-β-cyclodextrin (DM-β-CD) in vacuo and in water, as well as its ability to bind the antidepressant drug mianserin (MIA) in aqueous solution, are investigated computationally. The results are shown to depend strongly on the density functional theory (DFT) applied. The most stable conformers of DM-β-CD found with the B3LYP-GD2 method differ from these indicated by M062X-GD3 and other functionals. According to the latter, two crystal structures, ZULQAY and BOYFOK03, optimized in vacuo and in water, respectively, have the lowest energy. Both the B3LYP-GD2 and M062X-GD3 results show that all tested inclusion and noninclusion complexes of MIA:DM-β-CD in stoichiometry 1:1 are stable in water. However, the structures and their energetic properties obtained with each method differ: in the most stable configurations, different aromatic rings of MIA are embedded inside DM-β-CD, and the corresponding complexation energies (calculated with the 6-31++G(d,p) basis set and corrected for the basis set superposition error) are -29.6 (B3LYP-GD2) and -23.9 (M062X-GD3) kcal/mol. The NMR spectra of DM-β-CD and MIA:DM-β-CD are also compared.
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Affiliation(s)
- Anna Ignaczak
- Theoretical and Structural Chemistry Group, Department of Physical Chemistry, Faculty of Chemistry, University of Lodz, Pomorska 163/165, 90-236 Lodz, Poland
| | - Łukasz Orszański
- Theoretical and Structural Chemistry Group, Department of Physical Chemistry, Faculty of Chemistry, University of Lodz, Pomorska 163/165, 90-236 Lodz, Poland
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30
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Morency M, Néron S, Iftimie R, Wuest JD. Predicting p Ka Values of Quinols and Related Aromatic Compounds with Multiple OH Groups. J Org Chem 2021; 86:14444-14460. [PMID: 34613729 DOI: 10.1021/acs.joc.1c01279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quinonoid compounds play central roles as redox-active agents in photosynthesis and respiration and are also promising replacements for inorganic materials currently used in batteries. To design new quinonoid compounds and predict their state of protonation and redox behavior under various conditions, their pKa values must be known. Methods that can predict the pKa values of simple phenols cannot reliably handle complex analogues in which multiple OH groups are present and may form intramolecular hydrogen bonds. We have therefore developed a straightforward method based on a linear relationship between experimental pKa values and calculated differences in energy between quinols and their deprotonated forms. Simple adjustments allow reliable predictions of pKa values when intramolecular hydrogen bonds are present. Our approach has been validated by showing that predicted and experimental values for over 100 quinols and related compounds differ by an average of only 0.3 units. This accuracy makes it possible to select proper pKa values when experimental data vary, predict the acidity of quinols and related compounds before they are made, and determine the sites and orders of deprotonation in complex structures with multiple OH groups.
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Affiliation(s)
- Mathieu Morency
- Département de Chimie, Université de Montréal, Montréal, Québec H2V 0B3, Canada
| | - Sébastien Néron
- Département de Chimie, Université de Montréal, Montréal, Québec H2V 0B3, Canada
| | - Radu Iftimie
- Département de Chimie, Université de Montréal, Montréal, Québec H2V 0B3, Canada
| | - James D Wuest
- Département de Chimie, Université de Montréal, Montréal, Québec H2V 0B3, Canada
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31
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Jabłoński M, Krygowski TM. Dependence of the substituent energy on the level of theory. J Comput Chem 2021; 42:2079-2088. [PMID: 34432304 DOI: 10.1002/jcc.26738] [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: 05/06/2021] [Revised: 06/24/2021] [Accepted: 07/22/2021] [Indexed: 01/08/2023]
Abstract
Most often, the substituent effects are described using rather troublesome Hammett constants. Quite recently, it has been proposed to use the so-called substituent energy, which is based on total energies of the X-substituted polycyclic aromatic hydrocarbon and phenyl. This article concerns the influence of the applied level of theory (i.e., both the basis set and the method) on the determined values of the substituent energies. For this purpose, the energies of the NH2 and NO2 groups in 16 unique positions of naphthalene, anthracene, tetracene, phenanthrene, and pyrene were calculated using 10 different basis sets and 23 various exchange-correlation functionals representing the entire Jacob's Ladder, from local, through gradient- and meta-gradient-corrected, to hybrid and double-hybrid ones. Additionally, using even larger 6-311++G(2df,2p) basis set, the energies of NH2 , NO2 , CN, and Cl were also computed. Both the basis set and the method used have little effect on the substituent energy if the substituent is in the benzene-like position. On the contrary, the effect of the level of theory is pronounced especially in the case of the most spatially crowded 4-substituted phenanthrene. Substituent energies have been shown to be very useful theoretical parameters describing the proximity effect in the substituted derivatives of polycyclic aromatic hydrocarbons.
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Affiliation(s)
- Mirosław Jabłoński
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Toruń, Poland
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32
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Williams AE, Hammer NI, Tschumper GS. Relative energetics of CH 3CH 2O, CH 3CHOH, and CH 2CH 2OH radical products from ethanol dehydrogenation. J Chem Phys 2021; 155:114306. [PMID: 34551536 DOI: 10.1063/5.0062809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This study has examined the relative energetics of nine stationary points associated with the three different radical isomers generated by removing a H atom from ethanol at the O atom (ethoxy, CH3CH2O), the α C atom (CH3CHOH), and the β C atom (CH2CH2OH). For the first time, CCSD(T) geometry optimizations and harmonic vibrational frequency computations with the cc-pVTZ and aug-cc-pVTZ basis sets have been carried out to characterize two unique minima for each isomer along with three transition state structures with Cs symmetry. Explicitly correlated CCSD(T) computations were also performed to estimate the relative energetics of these nine stationary points near the complete basis set limit. These benchmark results were used to assess the performance of various density functional theory (DFT) and wave function theory methods, and they will help guide method selection for future studies of alcohols and their radicals. The structures generated by abstracting H from the α C atom have significantly lower electronic energies (by at least 7 kcal mol-1) than the CH3CH2O and CH2CH2OH radicals. Although previously reported as a minimum on the ground-state surface, the 2A″ Cs structure of the ethoxy radical was found to be a transition state in this study with MP2, CCSD(T), and a number of DFT methods. An implicit solvation model used in conjunction with DFT and MP2 methods did not qualitatively change the relative energies of the isomers, but the results suggest that the local minima for the CH3CHOH and CH2CH2OH radicals could become more energetically competitive in condensed phase environments, such as liquid water and ethanol.
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Affiliation(s)
- Ashley E Williams
- Department of Chemistry and Biochemistry, University of Mississippi, P.O. Box 1848, University, Mississippi 38677, USA
| | - Nathan I Hammer
- Department of Chemistry and Biochemistry, University of Mississippi, P.O. Box 1848, University, Mississippi 38677, USA
| | - Gregory S Tschumper
- Department of Chemistry and Biochemistry, University of Mississippi, P.O. Box 1848, University, Mississippi 38677, USA
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33
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Loipersberger M, Bertels LW, Lee J, Head-Gordon M. Exploring the Limits of Second- and Third-Order Møller-Plesset Perturbation Theories for Noncovalent Interactions: Revisiting MP2.5 and Assessing the Importance of Regularization and Reference Orbitals. J Chem Theory Comput 2021; 17:5582-5599. [PMID: 34382394 PMCID: PMC9948597 DOI: 10.1021/acs.jctc.1c00469] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
This work systematically assesses the influence of reference orbitals, regularization, and scaling on the performance of second- and third-order Møller-Plesset perturbation theory wave function methods for noncovalent interactions (NCIs). Testing on 19 data sets (A24, DS14, HB15, HSG, S22, X40, HW30, NC15, S66, AlkBind12, CO2Nitrogen16, HB49, Ionic43, TA13, XB18, Bauza30, CT20, XB51, and Orel26rad) covers a wide range of different NCIs including hydrogen bonding, dispersion, and halogen bonding. Inclusion of potential energy surfaces from different hydrogen bonds and dispersion-bound complexes gauges accuracy for nonequilibrium geometries. Fifteen methods are tested. In notation where nonstandard choices of orbitals are denoted as methods:orbitals, these are MP2, κ-MP2, SCS-MP2, OOMP2, κ-OOMP2, MP3, MP2.5, MP3:OOMP2, MP2.5:OOMP2, MP3:κ-OOMP2, MP2.5:κ-OOMP2, κ-MP3:κ-OOMP2, κ-MP2.5:κ-OOMP2, MP3:ωB97X-V, and MP2.5:ωB97X-V. Furthermore, we compare these methods to the ωB97M-V and B3LYP-D3 density functionals, as well as CCSD. We find that the κ-regularization (κ = 1.45 au was used throughout) improves the energetics in almost all data sets for both MP2 (in 17 out of 19 data sets) and OOMP2 (16 out of 19). The improvement is significant (e.g., the root-mean-square deviation (RMSD) for the S66 data set is 0.29 kcal/mol for κ-OOMP2 versus 0.67 kcal/mol for MP2) and for interactions between stable closed-shell molecules, not strongly dependent on the reference orbitals. Scaled MP3 (with a factor of 0.5) using κ-OOMP2 reference orbitals (MP2.5:κ-OOMP2) provides significantly more accurate results for NCIs across all data sets with noniterative O(N6) scaling (S66 data set RMSD: 0.10 kcal/mol). Across the entire data set of 356 points, the improvement over standard MP2.5 is approximately a factor of 2: RMSD for MP3:κ-OOMP2 is 0.25 vs 0.50 kcal/mol for MP2.5. The use of high-quality density functional reference orbitals (ωB97X-V) also significantly improves the results of MP2.5 for NCI over a Hartree-Fock orbital reference. All our assessments and conclusions are based on the use of the medium-sized aug-cc-pVTZ basis to yield results that are directly compared against complete basis set limit reference values.
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Affiliation(s)
| | - Luke W. Bertels
- Department of Chemistry, University of California, Berkeley, California 94720, USA,Present Address: Department of Chemistry, Virginia Tech, Blacksburg, VA 24061, USA
| | - Joonho Lee
- Department of Chemistry, University of California, Berkeley, California 94720, USA,Present Address: Department of Chemistry, Columbia University, NY
| | - Martin Head-Gordon
- 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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Ovchinnikov MY, Khursan SL. BEP-Like Correction of Nonequilibrium Thermodynamic Parameters of the Solvent-Assisted Reactions: The DFT and Ab Initio Study of Hydration, Peroxidation, and Enolization of Acetone and 1,1,1-Trifluoroacetone in Aqueous Solutions. J Phys Chem A 2021; 125:7369-7381. [PMID: 34410143 DOI: 10.1021/acs.jpca.1c04501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanisms of enolization and reactions of nucleophilic addition to carbonyl compounds were analyzed by density functional theory (DFT) (PBE1PBE) and ab initio (DLPNO-CCSD(T)) level of theory using the interaction of water and hydrogen peroxide with acetone and 1,1,1-trifluoroacetone (TFA) as the reference reactions. The transition states of the studied reactions were localized within the integrated approach that includes both the dielectric continuum theory (polarizable continuum model (PCM)) and the cyclic or two-cluster explicit solvation models. The considered models provide proton transfer in the enolization, hydration, and peroxidation reactions by the Grotthuss mechanism. It is shown that the calculated activation parameters at a sufficiently high level of theory and a sufficiently flexible solvation model can be additionally refined using the Bell-Evans-Polanyi (BEP)-like correction (in a form of the Bell-Evans-Polanyi equation), which is linear scaling of the model potential energy surface according to the equilibrium parameters of the reference reaction (experiment or high-level calculation). Quite good correspondence of the corrected and reference activation parameters and the lower sensitivity of the calculation results to the choice of the solvation model indicate the high reliability of the proposed BEP-like correction technique.
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Affiliation(s)
| | - Sergey L Khursan
- Ufa Institute of Chemistry UFRC RAS, 71 Prospect Oktyabrya, 450054 Ufa, Russia
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Masumian E, Nowroozi A, Nikparsa P, Zargari F. Theoretical evidence for the resonance-inhibited hydrogen bonding (RIHB) in enol-imine tautomers. Chem Phys 2021. [DOI: 10.1016/j.chemphys.2021.111255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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36
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Tesch R, Kowalski PM, Eikerling MH. Properties of the Pt(111)/electrolyte electrochemical interface studied with a hybrid DFT-solvation approach. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 33:444004. [PMID: 34348250 DOI: 10.1088/1361-648x/ac1aa2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
Self-consistent modeling of the interface between solid metal electrode and liquid electrolyte is a crucial challenge in computational electrochemistry. In this contribution, we adopt the effective screening medium reference interaction site method (ESM-RISM) to study the charged interface between a Pt(111) surface that is partially covered with chemisorbed oxygen and an aqueous acidic electrolyte. This method proves to be well suited to describe the chemisorption and charging state of the interface at controlled electrode potential. We present an in-depth assessment of the ESM-RISM parameterization and of the importance of computing near-surface water molecules explicitly at the quantum mechanical level. We found that ESM-RISM is able to reproduce some key interface properties, including the peculiar, non-monotonic charging relation of the Pt(111)/electrolyte interface. The comparison with independent theoretical models and explicit simulations of the interface reveals strengths and limitations of ESM-RISM for modeling electrochemical interfaces.
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Affiliation(s)
- Rebekka Tesch
- Institute of Energy and Climate Research, Theory and Computation of Energy Materials (IEK-13), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Chair of Theory and Computation of Energy Materials, Faculty of Georesources and Materials Engineering, RWTH Aachen University, 52062 Aachen, Germany
- Jülich Aachen Research Alliance, JARA-CSD and JARA-ENERGY, 52425 Jülich, Germany
| | - Piotr M Kowalski
- Institute of Energy and Climate Research, Theory and Computation of Energy Materials (IEK-13), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Jülich Aachen Research Alliance, JARA-CSD and JARA-ENERGY, 52425 Jülich, Germany
| | - Michael H Eikerling
- Institute of Energy and Climate Research, Theory and Computation of Energy Materials (IEK-13), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Chair of Theory and Computation of Energy Materials, Faculty of Georesources and Materials Engineering, RWTH Aachen University, 52062 Aachen, Germany
- Jülich Aachen Research Alliance, JARA-CSD and JARA-ENERGY, 52425 Jülich, Germany
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37
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Structural Water Stabilizes Protein Motifs in Liquid Protein Phase: The Folding Mechanism of Short β-Sheets Coupled to Phase Transition. Int J Mol Sci 2021; 22:ijms22168595. [PMID: 34445303 PMCID: PMC8395295 DOI: 10.3390/ijms22168595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 11/16/2022] Open
Abstract
Macromolecular associates, such as membraneless organelles or lipid-protein assemblies, provide a hydrophobic environment, i.e., a liquid protein phase (LP), where folding preferences can be drastically altered. LP as well as the associated phase change from water (W) is an intriguing phenomenon related to numerous biological processes and also possesses potential in nanotechnological applications. However, the energetic effects of a hydrophobic yet water-containing environment on protein folding are poorly understood. Here, we focus on small β-sheets, the key motifs of proteins, undergoing structural changes in liquid–liquid phase separation (LLPS) and also model the mechanism of energy-coupled unfolding, e.g., in proteases, during W → LP transition. Due to the importance of the accurate description for hydrogen bonding patterns, the employed models were studied by using quantum mechanical calculations. The results demonstrate that unfolding is energetically less favored in LP by ~0.3–0.5 kcal·mol−1 per residue in which the difference further increased by the presence of explicit structural water molecules, where the folded state was preferred by ~1.2–2.3 kcal·mol−1 per residue relative to that in W. Energetics at the LP/W interfaces was also addressed by theoretical isodesmic reactions. While the models predict folded state preference in LP, the unfolding from LP to W renders the process highly favorable since the unfolded end state has >1 kcal·mol−1 per residue excess stabilization.
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38
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Harder, better, faster, stronger: Large-scale QM and QM/MM for predictive modeling in enzymes and proteins. Curr Opin Struct Biol 2021; 72:9-17. [PMID: 34388673 DOI: 10.1016/j.sbi.2021.07.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/25/2021] [Accepted: 07/05/2021] [Indexed: 11/23/2022]
Abstract
Computational prediction of enzyme mechanism and protein function requires accurate physics-based models and suitable sampling. We discuss recent advances in large-scale quantum mechanical (QM) modeling of biochemical systems that have reduced the cost of high-accuracy models. Tradeoffs between sampling and accuracy have motivated modeling with molecular mechanics (MM) in a multiscale QM/MM or iterative approach. Limitations to both conventional density-functional theory and classical MM force fields remain for describing noncovalent interactions in comparison to experiment or wavefunction theory. Because predictions of enzyme action (i.e. electrostatics), free energy barriers, and mechanisms are sensitive to the protocol and embedding method in QM/MM, convergence tests and systematic methods for quantifying QM-level interactions are a needed, active area of development.
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39
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Valdiviezo J, Clever C, Beall E, Pearse A, Bae Y, Zhang P, Achim C, Beratan DN, Waldeck DH. Delocalization-Assisted Transport through Nucleic Acids in Molecular Junctions. Biochemistry 2021; 60:1368-1378. [PMID: 33870693 DOI: 10.1021/acs.biochem.1c00072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The flow of charge through molecules is central to the function of supramolecular machines, and charge transport in nucleic acids is implicated in molecular signaling and DNA repair. We examine the transport of electrons through nucleic acids to understand the interplay of resonant and nonresonant charge carrier transport mechanisms. This study reports STM break junction measurements of peptide nucleic acids (PNAs) with a G-block structure and contrasts the findings with previous results for DNA duplexes. The conductance of G-block PNA duplexes is much higher than that of the corresponding DNA duplexes of the same sequence; however, they do not display the strong even-odd dependence conductance oscillations found in G-block DNA. Theoretical analysis finds that the conductance oscillation magnitude in PNA is suppressed because of the increased level of electronic coupling interaction between G-blocks in PNA and the stronger PNA-electrode interaction compared to that in DNA duplexes. The strong interactions in the G-block PNA duplexes produce molecular conductances as high as 3% G0, where G0 is the quantum of conductance, for 5 nm duplexes.
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Affiliation(s)
- Jesús Valdiviezo
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Caleb Clever
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Edward Beall
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Pearse
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Yookyung Bae
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Peng Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Catalina Achim
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - David N Beratan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States.,Department of Physics, Duke University, Durham, North Carolina 27708, United States.,Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States
| | - David H Waldeck
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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40
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Abstract
Co-amorphous (CAM) systems are promising drug-delivery systems in the arena of therapeutic drug delivery, addressing the poor aqueous solubility of drugs by enhancing solubility and thereby improving the oral bioavailability and therapeutic effect of the drug. A CAM system is a single-phase homogeneous blend of two or more low molecular weight molecules that can be drug–drug or drug–co-former, stabilized via intermolecular interactions, adding the benefit of thermodynamic stability. This review covers the fundamentals of CAM systems and recent advances in formulation development. In particular, we strive to address the theoretical, molecular, technical and biopharmaceutical aspects, advantages over polymeric amorphous solid dispersions, mechanisms of stabilization of amorphous forms, insights into unexplored in silico tools in excipient selection and regulatory viewpoints.
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41
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Vennelakanti V, Qi HW, Mehmood R, Kulik HJ. When are two hydrogen bonds better than one? Accurate first-principles models explain the balance of hydrogen bond donors and acceptors found in proteins. Chem Sci 2021; 12:1147-1162. [PMID: 35382134 PMCID: PMC8908278 DOI: 10.1039/d0sc05084a] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/18/2020] [Indexed: 01/02/2023] Open
Abstract
Hydrogen bonds (HBs) play an essential role in the structure and catalytic action of enzymes, but a complete understanding of HBs in proteins challenges the resolution of modern structural (i.e., X-ray diffraction) techniques and mandates computationally demanding electronic structure methods from correlated wavefunction theory for predictive accuracy. Numerous amino acid sidechains contain functional groups (e.g., hydroxyls in Ser/Thr or Tyr and amides in Asn/Gln) that can act as either HB acceptors or donors (HBA/HBD) and even form simultaneous, ambifunctional HB interactions. To understand the relative energetic benefit of each interaction, we characterize the potential energy surfaces of representative model systems with accurate coupled cluster theory calculations. To reveal the relationship of these energetics to the balance of these interactions in proteins, we curate a set of 4000 HBs, of which >500 are ambifunctional HBs, in high-resolution protein structures. We show that our model systems accurately predict the favored HB structural properties. Differences are apparent in HBA/HBD preference for aromatic Tyr versus aliphatic Ser/Thr hydroxyls because Tyr forms significantly stronger O–H⋯O HBs than N–H⋯O HBs in contrast to comparable strengths of the two for Ser/Thr. Despite this residue-specific distinction, all models of residue pairs indicate an energetic benefit for simultaneous HBA and HBD interactions in an ambifunctional HB. Although the stabilization is less than the additive maximum due both to geometric constraints and many-body electronic effects, a wide range of ambifunctional HB geometries are more favorable than any single HB interaction. Correlated wavefunction theory predicts and high-resolution crystal structure analysis confirms the important, stabilizing effect of simultaneous hydrogen bond donor and acceptor interactions in proteins.![]()
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Affiliation(s)
- Vyshnavi Vennelakanti
- Department of Chemical Engineering
- Massachusetts Institute of Technology
- Cambridge
- USA
- Department of Chemistry
| | - Helena W. Qi
- Department of Chemical Engineering
- Massachusetts Institute of Technology
- Cambridge
- USA
- Department of Chemistry
| | - Rimsha Mehmood
- Department of Chemical Engineering
- Massachusetts Institute of Technology
- Cambridge
- USA
- Department of Chemistry
| | - Heather J. Kulik
- Department of Chemical Engineering
- Massachusetts Institute of Technology
- Cambridge
- USA
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42
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Chanajaree R, Sriuttha M, Lee VS, Wittayanarakul K. Thermodynamics and kinetics of cationic/anionic dyes adsorption on cross-linked chitosan. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114507] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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43
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Samala NR, Grinberg I. Tuning of ORR activity through the stabilization of the adsorbates by hydrogen bonding with substituent groups. Phys Chem Chem Phys 2020; 22:27811-27817. [PMID: 33245314 DOI: 10.1039/d0cp04478d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Metallocorroles and metalloporphyrins (M-N-C) are some of the best alternative molecular catalysts for the replacement of the expensive platinum-group metals (PGM) in oxygen reduction reaction (ORR) catalysis in polymer electrolyte membrane (PEM) fuel cells. To date, Co-based corroles have shown the best performance, but still suffer from the poor stability and the toxicity of the Co metal. Mn-N-C are more stable than Co-N-C, and are also less reactive towards peroxide formation. In this work, using first-principles density functional theory calculations, we study the improvement of the Mn-based corrole ORR activity by exploiting hydrogen bonding with substituent groups to modify the adsorption energies of the ORR intermediates and obtain higher onset potential (Vonset) values. We found that by using phenyl acetic acid as a substituent, Vonset increased from 0.54 V for the unsubstituted corrole to ∼0.9 V which is competitive with the Vonset of the Co-based corroles. Our results suggest that hydrogen bonding with substituent groups should be considered in the analysis and design of the reactivity of active sites in non-PGM ORR catalysts.
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44
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Skinner A, Yang C, Hincks K, Wang H, Resendiz MJE. Experimental and theoretical rationalization for the base pairing abilities of inosine, guanosine, adenosine, and their corresponding 8-oxo-7,8-dihydropurine, and 8-bromopurine analogues within A-form duplexes of RNA. Biopolymers 2020; 111:e23410. [PMID: 33216981 PMCID: PMC7780609 DOI: 10.1002/bip.23410] [Citation(s) in RCA: 4] [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: 09/20/2020] [Revised: 10/30/2020] [Accepted: 11/09/2020] [Indexed: 12/13/2022]
Abstract
Inosine is an important RNA modification, furthermore RNA oxidation has gained interest due, in part, to its potential role in the development/progression of disease as well as on its impact on RNA structure and function. In this report we established the base pairing abilities of purine nucleobases G, I, A, as well as their corresponding, 8-oxo-7,8-dihydropurine (common products of oxidation at the C8-position of purines), and 8-bromopurine (as probes to explore conformational changes), derivatives, namely 8-oxoG, 8-oxoI, 8-oxoA, 8-BrG, and 8-BrI. Dodecamers of RNA were obtained using standard phosphoramidite chemistry via solid-phase synthesis, and used as models to establish the impact that each of these nucleobases have on the thermal stability of duplexes, when base pairing to canonical and noncanonical nucleobases. Thermal stabilities were obtained from thermal denaturation transition (Tm ) measurements, via circular dichroism (CD). The results were then rationalized using models of base pairs between two monomers, via density functional theory (DFT), that allowed us to better understand potential contributions from H-bonding patterns arising from distinct conformations. Overall, some of the important results indicate that: (a) an anti-I:syn-A base pair provides thermal stability, due to the absence of the exocyclic amine; (b) 8-oxoG base pairs like U, and does not induce destabilization within the duplex when compared to the pyrimidine ring; (c) a U:G wobble-pair is only stabilized by G; and (d) 8-oxoA displays an inherited base pairing promiscuity in this sequence context. Gaining a better understanding of how this oxidatively generated lesions potentially base pair with other nucleobases will be useful to predict various biological outcomes, as well as in the design of biomaterials and/or nucleotide derivatives with biological potential.
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Affiliation(s)
- Austin Skinner
- Department of ChemistryUniversity of Colorado DenverDenverColoradoUSA
| | - Chou‐Hsun Yang
- Department of ChemistryUniversity of Colorado DenverDenverColoradoUSA
| | - Kazuki Hincks
- Department of ChemistryUniversity of Colorado DenverDenverColoradoUSA
| | - Haobin Wang
- Department of ChemistryUniversity of Colorado DenverDenverColoradoUSA
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Pinto AV, Magalhães AL. Intramolecular Hydrogen Bonds in Tip-Functionalized Single-Walled Carbon Nanotubes as pH-Sensitive Gates. J Phys Chem A 2020; 124:9542-9551. [PMID: 33169998 DOI: 10.1021/acs.jpca.0c03710] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Since their discovery, carbon nanotubes and other related nanomaterials are in the spotlight due to their unique molecular structures and properties, having a wide range of applications. The cage-like structure of carbon nanotubes is especially appealing as a route to confine molecules, isolating them from the solvent medium. This study aims to explore and characterize, through density functional theory (DFT) calculations, covalent tip-functionalization of single-walled carbon nanotubes (SWCNTS) with carboxymethyl moieties that establish pH sensitive molecular gates. The response of the molecular gate to pH fluctuations arises from variations in the noncovalent interactions between functionalized groups, which depend on the extent of protonation, leading to conformational changes. Overall, the hydrogen bonds present in the molecular models under study, as evaluated through topological analysis and pKa calculations, suggest that functionalized SWCNTs may be suitable for the design of drug delivery systems to enhance the efficiency of some pharmacological treatments, or even in the area of catalysis and separation processes, through their incorporation in nanocomposites.
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Affiliation(s)
- A V Pinto
- LAQV/Requimte, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - A L Magalhães
- LAQV/Requimte, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
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46
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Empel C, Jana S, Pei C, Nguyen TV, Koenigs RM. Photochemical O–H Functionalization of Aryldiazoacetates with Phenols via Proton Transfer. Org Lett 2020; 22:7225-7229. [DOI: 10.1021/acs.orglett.0c02564] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Claire Empel
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D-52074 Aachen, Germany
- School of Chemistry, University of New South Waley, Sydney 2052, Australia
| | - Sripati Jana
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D-52074 Aachen, Germany
| | - Chao Pei
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D-52074 Aachen, Germany
| | - Thanh Vinh Nguyen
- School of Chemistry, University of New South Waley, Sydney 2052, Australia
| | - Rene M. Koenigs
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D-52074 Aachen, Germany
- School of Chemistry, University of New South Waley, Sydney 2052, Australia
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47
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Abstract
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As
a field, computational toxicology is concerned with using in silico models to predict and understand the origins of
toxicity. It is fast, relatively inexpensive, and avoids the ethical
conundrum of using animals in scientific experimentation. In this
perspective, we discuss the importance of computational models in
toxicology, with a specific focus on the different model types that
can be used in predictive toxicological approaches toward mutagenicity
(SARs and QSARs). We then focus on how quantum chemical methods, such
as density functional theory (DFT), have previously been used in the
prediction of mutagenicity. It is then discussed how DFT allows for
the development of new chemical descriptors that focus on capturing
the steric and energetic effects that influence toxicological reactions.
We hope to demonstrate the role that DFT plays in understanding the
fundamental, intrinsic chemistry of toxicological reactions in predictive
toxicology.
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Affiliation(s)
- Piers A Townsend
- Centre for Sustainable Chemical Technologies, Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Matthew N Grayson
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
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48
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Hodgkinson P. NMR crystallography of molecular organics. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 118-119:10-53. [PMID: 32883448 DOI: 10.1016/j.pnmrs.2020.03.001] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 02/25/2020] [Accepted: 03/13/2020] [Indexed: 06/11/2023]
Abstract
Developments of NMR methodology to characterise the structures of molecular organic structures are reviewed, concentrating on the previous decade of research in which density functional theory-based calculations of NMR parameters in periodic solids have become widespread. With a focus on demonstrating the new structural insights provided, it is shown how "NMR crystallography" has been used in a spectrum of applications from resolving ambiguities in diffraction-derived structures (such as hydrogen atom positioning) to deriving complete structures in the absence of diffraction data. As well as comprehensively reviewing applications, the different aspects of the experimental and computational techniques used in NMR crystallography are surveyed. NMR crystallography is seen to be a rapidly maturing subject area that is increasingly appreciated by the wider crystallographic community.
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Affiliation(s)
- Paul Hodgkinson
- Department of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, UK.
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49
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Fabrizio A, Petraglia R, Corminboeuf C. Balancing Density Functional Theory Interaction Energies in Charged Dimers Precursors to Organic Semiconductors. J Chem Theory Comput 2020; 16:3530-3542. [DOI: 10.1021/acs.jctc.9b01193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Alberto Fabrizio
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Riccardo Petraglia
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Clemence Corminboeuf
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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50
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Zins EL. Microhydration of a Carbonyl Group: How does the Molecular Electrostatic Potential (MESP) Impact the Formation of (H 2O) n:(R 2C═O)Complexes? J Phys Chem A 2020; 124:1720-1734. [PMID: 32049521 DOI: 10.1021/acs.jpca.9b09992] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The presence of a carbonyl group in a molecule usually leads to the identification of a π-hole on the molecular electrostatic potential (MESP) of the species. How does this electrophilic site influence the formation of microhydrated complexes? To address this point, a panel of R2CO solutes with various MESPs was selected, and we identified the structures and properties of several complexes containing one, two, three and six water molecules. The following solutes were considered in the present study: H2CO, F2CO, Cl2CO,(NC)2CO and H2C═CO. Geometry optimizations and frequency calculations were carried out at the LC-ωPBE/6-311++G(d,p) level, with the GD3BJ empirical correction for dispersion. For a number of n water molecules around the R2CO solute, the structure and the features of the most stable (H2O)n:(R2CO) complexes are highly dependent on the MESP of the isolated R2CO solute. The formation of pi-hole bondings appears to play a decisive role in the initiation of a three-dimensional organization of water molecules around the solute.
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Affiliation(s)
- Emilie-Laure Zins
- De la Molécule aux Nano-Objets: Réactivité, Interactions Spectroscopies, MONARIS, CNRS, Sorbonne Université, 75005, Paris, France
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