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Shimpi MT, Sajjad M, Öberg S, Larsson JA. Physical binding energies using the electron localization function in 4-hydroxyphenylboronic acid co-crystals with aza donors. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2023; 35:505901. [PMID: 37659400 DOI: 10.1088/1361-648x/acf638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 09/01/2023] [Indexed: 09/04/2023]
Abstract
Binding energies are traditionally simulated using cluster models by computation of each synthon for each individual co-crystal former. However, our investigation of the binding strengths using the electron localization function (ELF) reveals that these can be determined directly from the crystal supercell computations. We propose a new modeling protocol for the computation of physical binding energies directly from bulk simulations using ELF analysis. In this work, we establish a correlation between ELF values and binding energies calculated for co-crystals of 4-hydroxyphenylboronic acid (4HPBA) with four different aza donors using density functional theory with varying descriptions of dispersion. Boronic acids are gaining significant interest in the field of crystal engineering, but theoretical studies on their use in materials are still very limited. Here, we present a systematic investigation of the non-covalent interactions in experimentally realized co-crystals. Prior diffraction studies on these complexes have shown the competitive nature between the boronic acid functional group and the para-substituted phenolic group forming heteromeric interactions with aza donors. We determine the stability of the co-crystals by simulating their lattice energies, and the different dispersion descriptions show similar trends in lattice energies and lattice parameters. Our study bolsters the experimental observation of the boronic acid group as a competitive co-crystal former in addition to the well-studied phenolic group. Further research on correlating ELF values for physical binding could potentially transform this approach to a viable alternative for the computation of binding energies.
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Affiliation(s)
- Mayura Talwelkar Shimpi
- Applied Physics, Division of Materials Science, Department of Engineering Sciences and Mathematics, Luleå University of Technology, SE-97187 Luleå, Sweden
- Department of Pharmaceutical Biosciences, Uppsala University, PO Box 591, 75124 Uppsala, Sweden
| | - Muhammad Sajjad
- Applied Physics, Division of Materials Science, Department of Engineering Sciences and Mathematics, Luleå University of Technology, SE-97187 Luleå, Sweden
- Nottingham Ningbo China Beacons of Excellence Research and Innovation Institute, University of Nottingham Ningbo China, Ningbo, People's Republic of China
| | - Sven Öberg
- Applied Physics, Division of Materials Science, Department of Engineering Sciences and Mathematics, Luleå University of Technology, SE-97187 Luleå, Sweden
| | - J Andreas Larsson
- Applied Physics, Division of Materials Science, Department of Engineering Sciences and Mathematics, Luleå University of Technology, SE-97187 Luleå, Sweden
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Markham GD, Rostami H, Larkin JD, Bock CW. Models for boronic acid receptors II: a computational structural, bonding, and thermochemical investigation of the RB(OH)2∙H2O∙NH3 and RB(−OCH2CH2O−)∙NH3∙H2O potential energy surfaces (R = H, methyl, phenyl, and ortho-methyl-phenyl). Struct Chem 2023. [DOI: 10.1007/s11224-023-02131-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
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Hernández-Paredes J, Olvera-Tapia AL, Arenas-García JI, Höpfl H, Morales-Rojas H, Herrera-Ruiz D, Gonzaga-Morales AI, Rodríguez-Fragoso L. On molecular complexes derived from amino acids and nicotinamides in combination with boronic acids. CrystEngComm 2015. [DOI: 10.1039/c4ce01934b] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Adamczyk-Woźniak A, Brzózka Z, Dąbrowski M, Madura ID, Scheidsbach R, Tomecka E, Żukowski K, Sporzyński A. Influence of the ortho-methoxyalkyl substituent on the properties of phenylboronic acids. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2012.09.049] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Bock CW, Larkin JD. Heats of Formation for the Boronic Acids R-B(OH) 2 and Boroxines R 3B 3O 3 (R=H, Li, HBe, H 2B, H 3C, H 2N, HO, F, and Cl) Calculated at the G2, G3, and G4 Levels of Theory. COMPUT THEOR CHEM 2012; 986:35-42. [PMID: 24653975 DOI: 10.1016/j.comptc.2012.02.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Boronic acids (R-B(OH)2) and their boroxine (R3B3O3) dehydration products have emerged as important classes of compounds with a multitude of diverse applications. However, the available heats of formation for these compounds are not always as accurate as would be required for further use. In this study the heats of formation at 298.15 K of R-B(OH)2 and R3B3O3 (R = H, Li, HBe, H2B, H3C, H2N, HO, F, and Cl) have been calculated at the G2, G3[G3B3], and G4 levels of theory and used to determine the enthalpy changes for the dehydration reactions: 3 R-B(OH)2 → R3B3O3 + 3 H2O; comparisons are made with other rigorous levels of theory, e.g. CBS-Q[CBS-QB3] and W1U, as well as with experimental values wherever possible. Enthalpy changes for the dehydration reactions have also been calculated using second-order Møller-Plesset perturbation theory (MP2) with the Dunning-Woon correlation-consistent aug-cc-pVDZ and aug-cc-pVTZ basis sets, and B3LYP density functional theory with the 6-311++G(2df,2pd) basis set. With the exception of H2N-B(OH)2, the dehydration reactions are consistently predicted to be exothermic. Our results provide a cautionary note for the use of the B3LYP functional in the calculation of structures and energies of boronic acids and boroxines. Where comparisons could be made, the G4 and W1U predictions for the heats of formation of these boron compounds differ significantly.
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Affiliation(s)
- Charles W Bock
- Department of Chemistry and Biochemistry, School of Science and Health, Philadelphia University, School House Lane and Henry Avenue, Philadelphia, PA 19144
| | - Joseph D Larkin
- The National Institutes of Health, National Heart, Lung and Blood Institute, Bldg. 50, Bethesda, MD 20851
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Cyrański MK, Klimentowska P, Rydzewska A, Serwatowski J, Sporzyński A, Stępień DK. Towards a monomeric structure of phenylboronic acid: The influence of ortho-alkoxy substituents on the crystal structure. CrystEngComm 2012. [DOI: 10.1039/c2ce25657f] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Tzeli D, Theodorakopoulos G, Petsalakis ID, Ajami D, Rebek J. Theoretical Study of Hydrogen Bonding in Homodimers and Heterodimers of Amide, Boronic Acid, and Carboxylic Acid, Free and in Encapsulation Complexes. J Am Chem Soc 2011; 133:16977-85. [DOI: 10.1021/ja206555d] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Demeter Tzeli
- Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou, Athens 116 35, Greece
| | - Giannoula Theodorakopoulos
- Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou, Athens 116 35, Greece
| | - Ioannis D. Petsalakis
- Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou, Athens 116 35, Greece
| | - Dariush Ajami
- The Skaggs Institute for Chemical Biology & Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Julius Rebek
- The Skaggs Institute for Chemical Biology & Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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Reinemann DN, Wright AM, Wolfe JD, Tschumper GS, Hammer NI. Vibrational Spectroscopy of N-Methyliminodiacetic Acid (MIDA)-Protected Boronate Ester: Examination of the B–N Dative Bond. J Phys Chem A 2011; 115:6426-31. [DOI: 10.1021/jp112016j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dana N. Reinemann
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Ashley M. Wright
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Jonathan D. Wolfe
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Gregory S. Tschumper
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Nathan I. Hammer
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
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Larkin JD, Markham GD, Milkevitch M, Brooks BR, Bock CW. Computational investigation of the oxidative deboronation of boroglycine, H2N-CH2-B(OH)2, Using H2O and H2O2. J Phys Chem A 2009; 113:11028-34. [PMID: 19810757 PMCID: PMC4219543 DOI: 10.1021/jp904149w] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report results from a computational investigation of the oxidative deboronation of boroglycine, H2N-CH2-B(OH)2, using H2O and H2O2 as the reactive oxygen species (ROS) to yield aminomethanol, H2N-CH2-OH; these results complement our study on the protodeboronation of boroglycine to produce methylamine, H2N-CH3 (Larkin et al. J. Phys. Chem. A 2007, 111, 6489-6500). Second-order Møller-Plesset (MP2) perturbation theory with Dunning-Woon correlation-consistent (cc) basis sets were used for the calculations with comparisons made to results from density functional theory (DFT) at the PBE1PBE/6-311++G(d,p)(cc-pVDZ) levels. The effects of a bulk aqueous environment were also incorporated into the calculations employing PCM and CPCM methodology. Using H2O as the ROS, the reaction H2O + H2N-CH2-B(OH)2 --> H2N-CH2-OH + H-B(OH)2 was calculated to be endothermic; the value of DeltaH(298)(0) was +12.0 kcal/mol at the MP2(FC)/cc-pVTZ computational level in vacuo and +13.7 kcal/mol in PCM aqueous media; the corresponding value for the activation barrier, DeltaH(double dagger), was +94.3 kcal/mol relative to the separated reactants in vacuo and +89.9 kcal/mol in PCM aqueous media. In contrast, the reaction H2O2 + H2N-CH2-B(OH)2 --> H2N-CH2-OH + B(OH)3 was calculated to be highly exothermic with an DeltaH(298)(0) value of -100.9 kcal/mol at the MP2(FC)/cc-pVTZ computational level in vacuo and -99.6 kcal/mol in CPCM aqueous media; the highest-energy transition state for the multistep process associated with this reaction involved the rearrangement of H2N-CH2-B(OH)(OOH) to H2N-CH2-O-B(OH)2 with a DeltaH(double dagger) value of +23.2 kcal/mol in vacuo relative to the separated reactants. These computational results for boroglycine are in accord with the experimental observations for the deboronation of the FDA approved anticancer drug bortezomib (Velcade, PS-341), where it was found to be the principle deactivation pathway (Labutti et al. Chem. Res. Toxicol. 2006, 19, 539-546).
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Affiliation(s)
- Joseph D. Larkin
- The National Institutes of Health, National Heart, Lung, and Blood Institute, 5635 Fishers Lane, Rockville, MD 20852
| | - George D. Markham
- The Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
| | - Matt Milkevitch
- Department of Chemistry and Biochemistry, School of Science and Health, Philadelphia University, School House Lane and Henry Avenue, Philadelphia, PA 19144
| | - Bernard R. Brooks
- The National Institutes of Health, National Heart, Lung, and Blood Institute, 5635 Fishers Lane, Rockville, MD 20852
| | - Charles W. Bock
- Department of Chemistry and Biochemistry, School of Science and Health, Philadelphia University, School House Lane and Henry Avenue, Philadelphia, PA 19144
- The Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
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Zoellner JM, Zoellner RW. Uncharged analogues of the phenalenyl cation: Hartree–Fock, Møller–Plesset, and density functional computational investigations of the isomers of boraphenalene. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.02.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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11
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Sandberg T, Hotokka M. Conformational analysis of hydroxymatairesinol in aqueous solution with molecular dynamics. J Comput Chem 2009; 30:2666-73. [PMID: 19396812 DOI: 10.1002/jcc.21293] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Molecular dynamics simulations were performed on the naturally occuring lignan hydroxymatairesinol (HMR) using the GROMACS software. The aim of this study was to explore the conformational behavior of HMR in aqueous solution adopting the TIP4P model. The topology of HMR was constructed by hand and HMR was modeled with the OPLS-AA force field implemented in GROMACS. The five torsional angles in HMR were properly analyzed during the simulations. Correlations through certain patterns were observed between the angles. The determining property for the conformation preferred in aqueous solution was found to be the dipole moment and not the lowest energy in gas phase. The solvation effects on HMR was also studied by quantum chemical calculations applying the COnductorlike Screening MOdel (COSMO), the results of which were compared with results from a previous study using the Polarized Continuum Model (PCM). In the present work, COSMO was found to give more credible relative energies than PCM.
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Affiliation(s)
- Thomas Sandberg
- Department of Physical Chemistry, Abo Akademi University, Porthansgatan 3-5, 20500 Abo, Turku, Finland
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Larkin JD, Bhat KL, Markham GD, James TD, Brooks BR, Bock CW. A computational characterization of boron-oxygen multiple bonding in HN=CH-CH=CH-NH-BO. J Phys Chem A 2008; 112:8446-54. [PMID: 18707068 DOI: 10.1021/jp800125p] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structures, relative energies, and bonding characteristics for various conformers of 3-imino-N-(oxoboryl)prop-1-en-1-amine, HN=CH-CH=CH-NH-BO, and the corresponding borocycle (-HN=CH-CH=CH-NH-B-)O are discussed using results from second-order Møller-Plesset (MP2) perturbation theory with the Dunning-Woon correlation-consistent cc-pVDZ, aug-cc-pVDZ, and cc-pVTZ basis sets. These MP2 results are compared to those from computationally efficient density functional theory (DFT) calculations using the LDA, PBE, TPSS, BLYP, B3LYP, BVP86, OLYP, O3LYP, and PBE1PBE functionals in conjunction with the economical Pople-type 6-311++G(d,p) basis set to evaluate the suitability of these DFT/6-311++G(d,p) levels for use with larger boron-containing systems. The effects of an aqueous environment were incorporated into the calculations using COSMO methodology. The calculated boron-oxygen bond lengths, orbital compositions, and bond orders in all the (acyclic) HN=CH-CH=CH-NH-BO conformers were consistent with the presence of a boron-oxygen triple bond, similar to that found in H-BO and H2N-BO. The (-HN=CH-CH=CH-NH-B-)O borocycle is predicted to be planar (C2v symmetry), and it is approximately 30 kcal/mol lower in energy than any of the (acyclic) HN=CH-CH=CH-NH-BO conformers; the boron-oxygen bond in this borocycle has significant double bond character, a bonding scheme for which there has been only one experimental structure reported in the literature (Vidovic, D. ; et al. J. Am. Chem. Soc. 2005, 127, 4566- 4569).
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Affiliation(s)
- Joseph D Larkin
- Department of Chemistry, Bloomsburg University of Pennsylvania, Bloomsburg, Pennsylvania 17815, USA.
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