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Ahirwar MB, Gadre SR, Deshmukh MM. Molecular Tailoring Approach for the Direct Estimation of Individual Noncovalent Interaction Energies in Molecular Systems. J Phys Chem A 2024. [PMID: 39037864 DOI: 10.1021/acs.jpca.4c01176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
The noncovalent interactions (NCIs) are omnipresent in chemistry, physics, and biology. The study of such interactions offers insights into various physicochemical phenomena. Some indirect approaches proposed in the literature for exploring the NCIs are briefly reviewed in Section 1 of this Perspective. These include: (i) Shift in the stretching frequency of an X-Y bond involved in X-Y···Z interaction. (ii) Topological analysis of molecular electron density. (iii) Empirical equations derived employing experimental and theoretical quantities. However, a direct method for estimating individual intramolecular/intermolecular interaction energies has been conspicuous by its absence from the literature. We have developed a molecular tailoring approach (MTA)-based method enabling a direct and reliable estimation of the energy of intra- as well as intermolecular interactions. This method offers a direct and reliable estimation of these interactions, in particular of the hydrogen bonds (HB) in molecules/weakly bound clusters along with the respective cooperativity contribution. In Section 2, the basis of our method is discussed, along with some illustrative examples. The application of this method to a variety of molecules and clusters, with a special emphasis on estimating the HB energy along with the energy of other NCIs is presented in Section 3. Section 4 discusses some computational strategies for applying our method to large molecular clusters. The last Section provides a summary and a discussion on future developments.
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Affiliation(s)
- Mini Bharati Ahirwar
- Department of Chemistry, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar 470003, India
| | - Shridhar R Gadre
- Department of Scientific Computing, Modelling, & Simulation, Savitribai Phule Pune University, Pune 411007, India
- Department of Chemistry, Savitribai Phule Pune University, Pune 411007, India
| | - Milind M Deshmukh
- Department of Chemistry, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar 470003, India
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2
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Afonin AV, Rusinska-Roszak D. Quantification of hydrogen bond energy based on equations using spectroscopic, structural, QTAIM-based, and NBO-based descriptors which calibrated by the molecular tailoring approach. J Mol Model 2023; 30:18. [PMID: 38159168 PMCID: PMC10757697 DOI: 10.1007/s00894-023-05811-1] [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: 11/11/2023] [Accepted: 12/12/2023] [Indexed: 01/03/2024]
Abstract
CONTEXT Hydrogen bonds critically influence the structure and properties of both organic molecules and biomolecules, as well as supramolecular assemblies. For this reason, the development and elaboration of methods for quantitative assessment of hydrogen bond energy is an urgent challenge. In this study, using a large series of hydroxycarbonyl aliphatic compounds with the O‒H···O = C intramolecular hydrogen bond, a bank of hydrogen bond descriptors was created, including spectroscopic, structural, QTAIM-based, and NBO-based parameters. It was shown that the O‒H vibration frequency, OH chemical shift as the spectroscopic descriptors, the O···H hydrogen bond length, O···O distance, and O‒H covalent bond length as the structural descriptors, the electron density and its Laplacian, electron potential energy density in the hydrogen bond critical point, the electron density at the ring critical point as the QTAIM-based descriptors change in a correlated manner. The same correlation is found in change of the charge transfer energy through a hydrogen bond, the occupancy of the O‒H bond antibonding orbital, the Wiberg indices of the O···H hydrogen bond, and the O‒H covalent bond, as well as the polarization of the O‒H bond, which are the NBO-based descriptors. It was also recognized that the specified descriptors from the spectroscopic, structural, QTAIM-based, and NBO-based categories are functionally related to the values of intramolecular hydrogen bond energy, quantified via the molecular tailoring approach. This allowed one to obtain a system of equations for quantitative estimation of intramolecular hydrogen bond energy based on the spectroscopic, structural, QTAIM, and NBO descriptors, which makes such quantification more dependable and reliable. METHODS To obtain the spectroscopic descriptors, the vibrational spectra and shielding constants were calculated using the GIAO method. Structural descriptors were obtained for the equilibrium geometry of molecules, calculated at the MP2(FC)/6-311 + + (2d,2p) level using the Gaussian 09 program. The QTAIM-based descriptors were calculated using the AIMAll program within the framework of the quantum theory "Atoms in Molecules." The NBO-based descriptors were calculated using the NBO 3.1 program implemented into Gaussian 09. To quantify the energy of intramolecular hydrogen bonds, molecular fragmentation was used within the molecular tailoring approach.
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Affiliation(s)
- Andrei V Afonin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Division of Russian Academy of Sciences, Irkutsk, Russia
| | - Danuta Rusinska-Roszak
- Institute of Chemical Technology and Engineering, Poznan University of Technology, Poznan, Poland.
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Revealing the Reasons for Degeneration of Resonance-Assisted Hydrogen Bond on the Aromatic Platform: Calculations of Ortho-, Meta-, Para-Disubstituted Benzenes, and ( Z)-( E)-Olefins. Molecules 2023; 28:molecules28020536. [PMID: 36677595 PMCID: PMC9860835 DOI: 10.3390/molecules28020536] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/22/2022] [Accepted: 12/26/2022] [Indexed: 01/06/2023] Open
Abstract
The energies of the O-H∙∙∙O=C intramolecular hydrogen bonds were compared quantitatively for the series of ortho-disubstituted benzenes and Z-isomers of olefins via a molecular tailoring approach. It was established that the hydrogen bond energy in the former series is significantly less than that in the latter one. The reason for lowering the hydrogen bond energy in the ortho-disubstituted benzenes compared to the Z-isomers of olefins is the decrease in the π-contribution to the total energy of the complex interaction, in which the hydrogen bond per se is enhanced by the resonance effect. By the example of the para- and meta-disubstituted benzenes, as well as E-isomers of olefins, it was explicitly shown that the aromatic ring is a much poorer conductor of the resonance effect compared to the double bond. The hydrogen bond in the ortho-disubstituted benzenes has a lower energy than a typical resonance-assisted hydrogen bond because the aromatic moiety cannot properly assist the hydrogen bond with a resonance effect. Thus, a hydrogen bond on an aromatic platform should fall into a special category, namely an aromaticity-assisted hydrogen bond, which is closer by nature to a simple hydrogen bond rather than to a resonance-assisted one.
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Afonin AV, Rusinska‐Roszak D. Molecular tailoring approach as tool for revealing resonance‐assisted hydrogen bond: Case study of
Z
‐pyrrolylenones with the NH⋯OС intramolecular hydrogen bond. J Comput Chem 2022; 43:1596-1607. [DOI: 10.1002/jcc.26960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/14/2022] [Accepted: 06/18/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Andrei V. Afonin
- A. E. Favorsky Irkutsk Institute of Chemistry Siberian Division of Russian Academy of Sciences Irkutsk Russia
| | - Danuta Rusinska‐Roszak
- Institute of Chemical Technology and Engineering Poznan University of Technology Poznan Poland
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Afonin AV, Rusinska-Roszak D. Guide to tuning the chalcone molecular properties based on the push-pull effect energy scale created via the molecular tailoring approach. J Comput Chem 2022; 43:631-643. [PMID: 35175632 DOI: 10.1002/jcc.26827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/23/2022] [Accepted: 02/03/2022] [Indexed: 12/18/2022]
Abstract
Using the molecular tailoring approach, a total energy scale for the push-pull effect in the range from -40 to 100 kcal/mol is created for the wide series of neutral, charged and doubly charged compounds on the chalcone platform. Taking into account similar energy scale for hydrogen bonds, the strength of the push-pull effect is ranked in the seven categories, ranging from negative (anti-push-pull) to very weak and very strong push-pull effect. It is demonstrated that the molecular properties of chalcone can be tuned prior synthesis due to the created energy scale for the push-pull effect. The single bonds of the π-spacer in the chalcones are shortened, the double ones are lengthened, and the C=O bond vibrations are red shifted when the push-pull effect is enhanced along the energy scale. The HOMO and LUMO energies change systematically while the HOMO-LUMO energy gap narrows as the strength of the push-pull effect increases.
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Affiliation(s)
- Andrei V Afonin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Division of Russian Academy of Sciences, Irkutsk, Russia
| | - Danuta Rusinska-Roszak
- Institute of Chemical Technology and Engineering, Poznan University of Technology, Poznan, Poland
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Gupta BS, Jelle BP, Gao T. In vitro cell composition identification of wood decay fungi by Fourier transform infrared spectroscopy. ROYAL SOCIETY OPEN SCIENCE 2022; 9:201935. [PMID: 35127108 PMCID: PMC8808097 DOI: 10.1098/rsos.201935] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
Decay pathogens follow dissimilar metabolic mechanisms to cause irreversible damage to woody tissues. The objective of this study is to perform inter- and intra-species microbial cell structural comparison using attenuated total reflectance Fourier transform infrared spectroscopy. Representative fungi species, causing brown rot and white rot, namely, Postia placenta and Trametes versicolor, respectively, were cultured in laboratory conditions. In vitro spectral measurements were performed at periodic two week intervals of fungal growth. The study shows structural differences for both species of fungi. The prominent presence of protein amide, carbohydrate and carboxyl bands was of interest. Spectral deconvolution of the infrared broadband around approximately 3300 cm-1 produced peaks at four different wavenumbers. The hydrogen bond energy obtained at the four wavenumbers, from deconvolution, varied from approximately 41 kJ mol-1 to approximately 7 kJ mol-1, indicating the presence of strong and weak forces in microbial cell structure. The hydrogen bond distance, obtained at the deconvoluted wavenumbers, varied between 2.7 Å-2.8 Å, indicating the presence of short and long-distance forces within microbial cells. Microscopic observation showed mycelium colonization, hyphal tip and lateral branching.
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Affiliation(s)
- Barun Shankar Gupta
- Department of Civil and Environmental Engineering, Norwegian University of Science and Technology (NTNU), Høgskoleringen 7A, 7491 Trondheim, Norway
| | - Bjørn Petter Jelle
- Department of Civil and Environmental Engineering, Norwegian University of Science and Technology (NTNU), Høgskoleringen 7A, 7491 Trondheim, Norway
| | - Tao Gao
- Department of Civil and Environmental Engineering, Norwegian University of Science and Technology (NTNU), Høgskoleringen 7A, 7491 Trondheim, Norway
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Gupta AK, Gamoke BC, Raghavachari K. Interaction-Deletion: A Composite Energy Method for the Optimization of Molecular Systems Selectively Removing Specific Nonbonded Interactions. J Phys Chem A 2021; 125:4668-4682. [PMID: 34014684 DOI: 10.1021/acs.jpca.1c02918] [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
The complex interactions between different portions of a large molecule can be challenging to analyze through traditional electronic structure calculations. Moreover, standard methods cannot easily quantify the physical consequences of individual pairwise interactions inside a molecule. By creating a set of molecular fragments, we propose a composite energy method to explore changes in a molecule caused by removing selected nonbonded interactions between different molecular portions. Energies and forces are easily obtained with this composite approach, allowing geometry optimizations that lead to chemically meaningful structures that describe how the omitted interactions contribute to changes in the local geometrical minima. We illustrate the application of our new hybrid scheme by computing the influence of intramolecular hydrogen-bonding interactions in two small molecules: 1,6-(tG+G+TG+G+g-)-hexanediol and a cyclic analogue, cis-1,4-cyclohexanediol. The resulting structural and energetic changes are interpreted to yield key physical insights and quantify concepts such as "preparation energy" or "reorganization energy". We demonstrate that the composite method can be extended to larger molecular systems by showing its application on a Si(100) surface model containing interactions between dissociated ammonia molecules on adjacent surface dimers. The scheme's efficacy is also tested by applying it to systems having multiple intramolecular interactions, viz., 310-polyglycine and H+GPGG. Furthermore, the cooperative nature of intramolecular hydrogen bonds is explored by using interaction-deletion in 2-nitrobenzene-1,3-diol.
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Affiliation(s)
- Ankur K Gupta
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Benjamin C Gamoke
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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8
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Molecular Tailoring Approach for the Estimation of Intramolecular Hydrogen Bond Energy. Molecules 2021; 26:molecules26102928. [PMID: 34069140 PMCID: PMC8155843 DOI: 10.3390/molecules26102928] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 11/29/2022] Open
Abstract
Hydrogen bonds (HBs) play a crucial role in many physicochemical and biological processes. Theoretical methods can reliably estimate the intermolecular HB energies. However, the methods for the quantification of intramolecular HB (IHB) energy available in the literature are mostly empirical or indirect and limited only to evaluating the energy of a single HB. During the past decade, the authors have developed a direct procedure for the IHB energy estimation based on the molecular tailoring approach (MTA), a fragmentation method. This MTA-based method can yield a reliable estimate of individual IHB energy in a system containing multiple H-bonds. After explaining and illustrating the methodology of MTA, we present its use for the IHB energy estimation in molecules and clusters. We also discuss the use of this method by other researchers as a standard, state-of-the-art method for estimating IHB energy as well as those of other noncovalent interactions.
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9
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Bhattacharyya S, Ghosh S, Wategaonkar S. O-H stretching frequency red shifts do not correlate with the dissociation energies in the dimethylether and dimethylsulfide complexes of phenol derivatives. Phys Chem Chem Phys 2021; 23:5718-5739. [PMID: 33662068 DOI: 10.1039/d0cp01589j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this perspective, we present a comprehensive report on the spectroscopic and computational investigations of the hydrogen bonded (H-bonded) complexes of Me2O and Me2S with seven para-substituted H-bond donor phenols. The salient finding was that although the dissociation energies, D0, of the Me2O complexes were consistently higher than those of the analogous Me2S complexes, the red-shifts in phenolic O-H frequencies, Δν(O-H), showed the exactly opposite trend. This is in contravention of the general perception that the red shift in the X-H stretching frequency in the X-HY hydrogen bonded complexes is a reliable indicator of H-bond strength (D0), a concept popularly known as the Badger-Bauer rule. This is also in contrast to the trend reported for the H-bonded complexes of H2S/H2O with several para substituted phenols of different pKa values wherein the oxygen centered hydrogen bonded (OCHB) complexes consistently showed higher Δν(O-H) and D0 compared to those of the analogous sulfur centered hydrogen bonded (SCHB) complexes. Our effort was to understand these intriguing observations based on the spectroscopic investigations of 1 : 1 complexes in combination with a variety of high level quantum chemical calculations. Ab initio calculations at the MP2 level and the DFT calculations using various dispersion corrected density functionals (including DFT-D3) were performed on counterpoise corrected surfaces to compute the dissociation energy, D0, of the H-bonded complexes. The importance of anharmonic frequency computations is underscored as they were able to correctly reproduce the observed trend in the relative OH frequency shifts unlike the harmonic frequency computations. We have attempted to find a unified correlation that would globally fit the observed red shifts in the O-H frequency with the H-bonding strength for the four bases, namely, H2S, H2O, Me2O, and Me2S, in this set of H-bond donors. It was found that the proton affinity normalized Δν(O-H) values scale very well with the H-bond strength.
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Affiliation(s)
- Surjendu Bhattacharyya
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India.
| | - Sanat Ghosh
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India.
| | - Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India.
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10
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Lozynski M, Rusinska-Roszak D. Finding the direct energy-structure correlations in intramolecular aromaticity assisted hydrogen bonding (AAHB). J Mol Graph Model 2021; 105:107884. [PMID: 33725643 DOI: 10.1016/j.jmgm.2021.107884] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 02/25/2021] [Accepted: 02/25/2021] [Indexed: 11/25/2022]
Abstract
A predictive model for intramolecular hydrogen bond energy (EHB) calculation of polyaromatic ortho-hydroxyaldehydes based on a set of small, functionalized hydrocarbons is developed. The complete data set of 18 compounds was used for this study. The model is based on one of four optional categories of molecular descriptors: geometric, spectroscopic, bond order and topological indices. The model of Wiberg bond indices (WBIs) as descriptors of the CC involved bond based on stepwise regression has acceptable prediction abilities for 14 structures of ortho-hydroxyformylobenzo[a]pyrene derivatives already at the semiempirical level. The presented correlation enables a significantly more rapid and quantitative description of the hydrogen bonding strength than the much more time-consuming MTA method. Thus, WBIs are shown to provide a reliable means for fast prescreening of the energy of chelate hydrogen bonds potentially for any polyaromatic derivatives.
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Affiliation(s)
- Marek Lozynski
- Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, 60-965, Poznan, Poland
| | - Danuta Rusinska-Roszak
- Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, 60-965, Poznan, Poland.
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Abstract
The method to calculate the energy of intramolecular hydrogen bond is proposed and tested for a sample of malonaldehyde and its fluorine derivatives; the corresponding calculations were performed at the ωB97XD/aug-cc-pVTZ level. This method based on relationships found for related intermolecular hydrogen bonds is compared with other approaches which may be applied to estimate the intramolecular hydrogen bond energy. Particularly, methods based on the comparison of the system that contains the intramolecular hydrogen bond compared with corresponding conformations where such interaction does not occur are discussed. The function-based energy decomposition analysis, FB-EDA, of the intramolecular hydrogen bonds is also proposed here.
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12
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Rosenberg RE, Chapman BK, Ferrill RN, Jung ES, Samaan CA. Approximating the Strength of the Intramolecular Hydrogen Bond in 2-Fluorophenol and Related Compounds: A New Application of a Classic Technique. J Phys Chem A 2020; 124:3851-3858. [PMID: 32312049 DOI: 10.1021/acs.jpca.0c01641] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Fluorinated organic compounds are ubiquitous in the pharmaceutical and agricultural industries. To better discern the mode of action of these compounds, it is critical to understand the strengths of hydrogen bonds involving fluorine. While established techniques can determine these strengths for intermolecular complexes, there is no analogous scheme for intramolecular hydrogen bonds. This work uses 1H nuclear magnetic resonance spectroscopy to measure the strength of intramolecular hydrogen bonds in ortho-substituted phenols. Titration of each phenol with DMSO in CCl4 yields a free energy of binding (ΔG). Subtraction of this value from the ΔG of binding of the standard, 4-fluorophenol, is shown to give the difference in ΔG for the cis and trans isomers of the ortho-substituted phenols. This difference is conventionally taken to be approximately equal to the ΔG of the intramolecular hydrogen bond. These data complement theoretical methods, which yield slightly larger ΔGs. Both theory and experiment point to a weak intramolecular hydrogen bond in 2-fluorophenol. The other 2-X-phenols have stronger hydrogen bonds, following the order F < Cl ≈ Br < OCH3. The methodology developed here can be readily applied to other systems with intramolecular hydrogen bonds.
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Affiliation(s)
- Robert E Rosenberg
- Department of Chemistry, Transylvania University,300 North Broadway, Lexington, Kentucky 40508, United States
| | - Bradley K Chapman
- Department of Chemistry, Transylvania University,300 North Broadway, Lexington, Kentucky 40508, United States
| | - Rachel N Ferrill
- Department of Chemistry, Transylvania University,300 North Broadway, Lexington, Kentucky 40508, United States
| | - Eiu Suk Jung
- Department of Chemistry, Transylvania University,300 North Broadway, Lexington, Kentucky 40508, United States
| | - Chris A Samaan
- Department of Chemistry, Transylvania University,300 North Broadway, Lexington, Kentucky 40508, United States
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Afonin AV, Vashchenko AV. Quantitative decomposition of resonance-assisted hydrogen bond energy in β-diketones into resonance and hydrogen bonding (π- and σ-) components using molecular tailoring and function-based approaches. J Comput Chem 2020; 41:1285-1298. [PMID: 32061114 DOI: 10.1002/jcc.26175] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 02/03/2020] [Indexed: 01/07/2023]
Abstract
Using the molecular tailoring and function-based approaches allows one to divide the energy of the O─H⋯O═C resonance-assisted hydrogen bond in a series of the β-diketones into resonance and hydrogen bonding components. The magnitude of the resonance component is assessed as about 6 kcal mol-1 . This value increases by ca. 1 kcal mol-1 on going from the weak to strong resonance-assisted hydrogen bonding. The magnitude of the hydrogen bonding component varies in the wide range from 2 to 20 kcal mol-1 depending on the structure of the β-diketone in question.
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Affiliation(s)
- Andrei V Afonin
- Institute of Chemistry, Siberian Division of Russian Academy of Sciences, Irkutsk, Russia
| | - Alexander V Vashchenko
- Institute of Chemistry, Siberian Division of Russian Academy of Sciences, Irkutsk, Russia
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14
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Afonin AV, Rusinska-Roszak D. A molecular tailoring approach – a new guide to quantify the energy of push–pull effects: a case study on (E)-3-(1H-pyrrol-2-yl)prop-2-enones. Phys Chem Chem Phys 2020; 22:22190-22194. [DOI: 10.1039/d0cp04432f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We report a new approach to quantify the push–pull effect in molecules with internal charge transfer.
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Affiliation(s)
- Andrei V. Afonin
- A. E. Favorsky Irkutsk Institute of Chemistry
- Siberian Division of Russian Academy of Sciences
- Irkutsk 664033
- Russian Federation
| | - Danuta Rusinska-Roszak
- Institute of Chemical Technology and Engineering
- Poznan University of Technology
- Poznan 60-965
- Poland
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15
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Singh V, Ibnusaud I, Gadre SR, Deshmukh MM. Fragmentation method reveals a wide spectrum of intramolecular hydrogen bond energies in antioxidant natural products. NEW J CHEM 2020. [DOI: 10.1039/d0nj00304b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Very strong and weak IHBs in curcumin.
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Affiliation(s)
- Vijay Singh
- Department of Chemistry
- Dr. Harisingh Gour Vishwavidyalaya (A Central University)
- Sagar
- India
| | - Ibrahim Ibnusaud
- Institute for Intensive Research in Basic Sciences
- Mahatma Gandhi University Campus
- P.O. Kottayam
- India
| | - Shridhar R. Gadre
- Interdisciplinary School of Scientific Computing and Department of Chemistry
- Savitribai Phule Pune University
- Pune 411 007
- India
| | - Milind M. Deshmukh
- Department of Chemistry
- Dr. Harisingh Gour Vishwavidyalaya (A Central University)
- Sagar
- India
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16
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Durka K, Górski B, Błocki K, Urban M, Woźniak K, Barbasiewicz M, Luliński S. Experimental and Theoretical Insights into Molecular and Solid-State Properties of Isomeric Bis(salicylaldehydes). J Phys Chem A 2019; 123:8674-8689. [DOI: 10.1021/acs.jpca.9b07360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Krzysztof Durka
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Bartosz Górski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Krzysztof Błocki
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Mateusz Urban
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Michał Barbasiewicz
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Sergiusz Luliński
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
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17
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On the performance of molecular tailoring approach for estimation of the intramolecular hydrogen bond energies of RAHB systems: a comparative study. Struct Chem 2019. [DOI: 10.1007/s11224-019-01415-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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18
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Bauer CA. How to Model Inter- and Intramolecular Hydrogen Bond Strengths with Quantum Chemistry. J Chem Inf Model 2019; 59:3735-3743. [DOI: 10.1021/acs.jcim.9b00132] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Cis/Trans Energetics in Epoxide, Thiirane, Aziridine and Phosphirane Containing Cyclopentanols: Effects of Intramolecular OH⋯O, S, N and P Contacts. Molecules 2019; 24:molecules24142523. [PMID: 31295845 PMCID: PMC6680949 DOI: 10.3390/molecules24142523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 06/24/2019] [Accepted: 07/03/2019] [Indexed: 02/01/2023] Open
Abstract
A recent computational analysis of the stabilizing intramolecular OH⋯O contact in 1,2-dialkyl-2,3-epoxycyclopentanol diastereomers has been extended to thiiriane, aziridine and phosphirane analogues. Density functional theory (DFT), second-order Møller-Plesset perturbation theory (MP2) and CCSD(T) coupled-cluster computations with simple methyl and ethyl substituents indicate that electronic energies of the cis isomers are lowered by roughly 3 to 4 kcal mol−1 when the OH group of these cyclopentanol systems forms an intramolecular contact with the O, S, N or P atom on the adjacent carbon. The results also suggest that S and P can participate in these stabilizing intramolecular interactions as effectively as O and N in constrained molecular environments. The stabilizing intramolecular OH⋯O, OH⋯S, OH⋯N and OH⋯P contacts also increase the covalent OH bond length and significantly decrease the OH stretching vibrational frequency in every system with shifts typically on the order of −41 cm−1.
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An insight into intramolecular blue-shifting C H⋯π hydrogen bonds in 1,3-hexadien-5-yne and its halogen-substituted derivatives. Chem Phys 2019. [DOI: 10.1016/j.chemphys.2018.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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21
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Afonin AV, Sterkhova IV, Vashchenko AV, Sigalov MV. Estimating the energy of intramolecular bifurcated (three-centered) hydrogen bond by X-ray, IR and 1 H NMR spectroscopy, and QTAIM calculations. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.02.106] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Matsui T, Yamamoto K, Fujita T, Morihashi K. Molecular Dynamics and Quantum Chemical Approach for the Estimation of an Intramolecular Hydrogen Bond Strength in Okadaic Acid. J Phys Chem B 2018; 122:7233-7242. [DOI: 10.1021/acs.jpcb.8b03272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Afonin AV, Vashchenko AV, Sigalov MV. Estimating the energy of intramolecular hydrogen bonds from 1H NMR and QTAIM calculations. Org Biomol Chem 2018; 14:11199-11211. [PMID: 27841888 DOI: 10.1039/c6ob01604a] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The values of the downfield chemical shift of the bridge hydrogen atom were estimated for a series of compounds containing an intramolecular hydrogen bond O-HO, O-HN, O-HHal, N-HO, N-HN, C-HO, C-HN and C-HHal. Based on these values, the empirical estimation of the hydrogen bond energy was obtained by using known relationships. For the compounds containing an intramolecular hydrogen bond, the DFT B3LYP/6-311++G(d,p) method was used both for geometry optimization and for QTAIM calculations of the topological parameters (electron density ρBCP and the density of potential energy V in the critical point of the hydrogen bond). The calculated geometric and topological parameters of hydrogen bonds were also used to evaluate the energy of the hydrogen bond based on the equations from the literature. Comparison of calibrating energies from the 1H NMR data with the energies predicted by calculations showed that the most reliable are the linear dependence on the topological ρBCP and V parameters. However, the correct prediction of the hydrogen bond energy is determined by proper fitting of the linear regression coefficients. To obtain them, new linear relationships were found between the calculated ρBCP and V parameters and the hydrogen bond energies obtained from empirical 1H NMR data. These relationships allow the comparison of the energies of different types of hydrogen bonds for various molecules and biological ensembles.
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Affiliation(s)
- Andrei V Afonin
- Institute of Chemistry, Siberian Division of Russian Academy of Sciences, 664033 Irkutsk, Russia.
| | - Alexander V Vashchenko
- Institute of Chemistry, Siberian Division of Russian Academy of Sciences, 664033 Irkutsk, Russia.
| | - Mark V Sigalov
- Department of Chemistry, Ben-Gurion University of the Negev, 84104, Beer Sheva, Israel.
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Widner DL, Robinson ER, Perez AB, Vang HG, Thorson RA, Driscoll ZL, Giebel SM, Berndt CW, Bosch E, Speetzen ED, Bowling NP. Comparing Strong and Weak Halogen Bonding in Solution:
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C NMR, UV/Vis, Crystallographic, and Computational Studies of an Intramolecular Model. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700969] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Danielle L. Widner
- Department of Chemistry University of Wisconsin‐Stevens Point 2001 Fourth Avenue WI 54481 Stevens Point US
| | - Emily R. Robinson
- Department of Chemistry University of Wisconsin‐Stevens Point 2001 Fourth Avenue WI 54481 Stevens Point US
| | - Alejandra B. Perez
- Department of Chemistry University of Wisconsin‐Stevens Point 2001 Fourth Avenue WI 54481 Stevens Point US
| | - Herh G. Vang
- Department of Chemistry University of Wisconsin‐Stevens Point 2001 Fourth Avenue WI 54481 Stevens Point US
| | - Rachel A. Thorson
- Department of Chemistry University of Wisconsin‐Stevens Point 2001 Fourth Avenue WI 54481 Stevens Point US
| | - Zakarias L. Driscoll
- Department of Chemistry University of Wisconsin‐Stevens Point 2001 Fourth Avenue WI 54481 Stevens Point US
| | - Sierra M. Giebel
- Department of Chemistry University of Wisconsin‐Stevens Point 2001 Fourth Avenue WI 54481 Stevens Point US
| | - Calvin W. Berndt
- Department of Chemistry University of Wisconsin‐Stevens Point 2001 Fourth Avenue WI 54481 Stevens Point US
| | - Eric Bosch
- Department of Chemistry Missouri State University 901 S. National Ave. MO 65897 Springfield US
| | - Erin D. Speetzen
- Department of Chemistry University of Wisconsin‐Stevens Point 2001 Fourth Avenue WI 54481 Stevens Point US
| | - Nathan P. Bowling
- Department of Chemistry University of Wisconsin‐Stevens Point 2001 Fourth Avenue WI 54481 Stevens Point US
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Rusinska-Roszak D. Energy of Intramolecular Hydrogen Bonding in ortho-Hydroxybenzaldehydes, Phenones and Quinones. Transfer of Aromaticity from ipso-Benzene Ring to the Enol System(s). Molecules 2017; 22:E481. [PMID: 28335484 PMCID: PMC6155192 DOI: 10.3390/molecules22030481] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/13/2017] [Accepted: 03/15/2017] [Indexed: 01/10/2023] Open
Abstract
Intramolecular hydrogen bonding (HB) is one of the most studied noncovalent interactions of molecules. Many physical, spectral, and topological properties of compounds are under the influence of HB, and there are many parameters used to notice and to describe these changes. Hitherto, no general method of measurement of the energy of intramolecular hydrogen bond (EHB) has been put into effect. We propose the molecular tailoring approach (MTA) for EHB calculation, modified to apply it to Ar-O-H∙∙∙O=C systems. The method, based on quantum calculations, was checked earlier for hydroxycarbonyl-saturated compounds, and for structures with resonance-assisted hydrogen bonding (RAHB). For phenolic compounds, the accuracy, repeatability, and applicability of the method is now confirmed for nearly 140 structures. For each structure its aromaticity HOMA indices were calculated for the central (ipso) ring and for the quasiaromatic rings given by intramolecular HB. The comparison of calculated HB energies and values of estimated aromaticity indices allowed us to observe, in some substituted phenols and quinones, the phenomenon of transfer of aromaticity from the ipso-ring to the H-bonded ring via the effect of electron delocalization.
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Affiliation(s)
- Danuta Rusinska-Roszak
- Institute of Chemical Technology and Engineering, Poznan University of Technology, ul. Berdychowo 4, 60-965 Poznan, Poland.
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Assessment of the Presence and Strength of H-Bonds by Means of Corrected NMR. Molecules 2016; 21:molecules21111426. [PMID: 27801801 PMCID: PMC6274571 DOI: 10.3390/molecules21111426] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 10/19/2016] [Accepted: 10/21/2016] [Indexed: 11/30/2022] Open
Abstract
The downfield shift of the NMR signal of the bridging proton in a H-bond (HB) is composed of two elements. The formation of the HB causes charge transfer and polarization that lead to a deshielding. A second factor is the mere presence of the proton-accepting group, whose electron density and response to an external magnetic field induce effects at the position of the bridging proton, exclusive of any H-bonding phenomenon. This second positional shielding must be subtracted from the full observed shift in order to assess the deshielding of the proton caused purely by HB formation. This concept is applied to a number of H-bonded systems, both intramolecular and intermolecular. When the positional shielding is removed, the remaining chemical shift is in much better coincidence with other measures of HB strength.
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Saha A, Raghavachari K. Analysis of Different Fragmentation Strategies on a Variety of Large Peptides: Implementation of a Low Level of Theory in Fragment-Based Methods Can Be a Crucial Factor. J Chem Theory Comput 2016; 11:2012-23. [PMID: 26574406 DOI: 10.1021/ct501045s] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We have investigated the performance of two classes of fragmentation methods developed in our group (Molecules-in-Molecules (MIM) and Many-Overlapping-Body (MOB) expansion), to reproduce the unfragmented MP2 energies on a test set composed of 10 small to large biomolecules. They have also been assessed to recover the relative energies of different motifs of the acetyl(ala)18NH2 system. Performance of different bond-cutting environments and the use of Hartree-Fock and different density functionals (as a low level of theory) in conjunction with the fragmentation strategies have been analyzed. Our investigation shows that while a low level of theory (for recovering long-range interactions) may not be necessary for small peptides, it provides a very effective strategy to accurately reproduce the total and relative energies of larger peptides such as the different motifs of the acetyl(ala)18NH2 system. Employing M06-2X as the low level of theory, the calculated mean total energy deviation (maximum deviation) in the total MP2 energies for the 10 molecules in the test set at MIM(d=3.5Å), MIM(η=9), and MOB(d=5Å) are 1.16 (2.31), 0.72 (1.87), and 0.43 (2.02) kcal/mol, respectively. The excellent performance suggests that such fragment-based methods should be of general use for the computation of accurate energies of large biomolecular systems.
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Affiliation(s)
- Arjun Saha
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States
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Mahmudov KT, Pombeiro AJL. Resonance-Assisted Hydrogen Bonding as a Driving Force in Synthesis and a Synthon in the Design of Materials. Chemistry 2016; 22:16356-16398. [PMID: 27492126 DOI: 10.1002/chem.201601766] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Indexed: 11/08/2022]
Abstract
Resonance-assisted hydrogen bonding (RAHB), a concept introduced by Gilli and co-workers in 1989, concerns a kind of intramolecular H-bonding strengthened by a conjugated π-system, usually in 6-, 8-, or 10-membered rings. This Review highlights the involvement of RAHB as a driving force in the synthesis of organic, coordination, and organometallic compounds, as a handy tool in the activation of covalent bonds, and in starting moieties for synthetic transformations. The unique roles of RAHB in molecular recognition and switches, E/Z isomeric resolution, racemization and epimerization of amino acids and chiral amino alcohols, solvatochromism, liquid-crystalline compounds, and in synthons for crystal engineering and polymer materials are also discussed. The Review can provide practical guidance for synthetic chemists that are interested in exploring and further developing RAHB-assisted synthesis and design of materials.
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Affiliation(s)
- Kamran T Mahmudov
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisboa, Portugal. .,Department of Chemistry, Baku State University, Z. Xalilov Str. 23, Az 1148, Baku, Azerbaijan.
| | - Armando J L Pombeiro
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisboa, Portugal.
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Madeira PP, Bessa A, Loureiro JA, Álvares-Ribeiro L, Rodrigues AE, Zaslavsky BY. Cooperativity between various types of polar solute–solvent interactions in aqueous media. J Chromatogr A 2015; 1408:108-17. [DOI: 10.1016/j.chroma.2015.07.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 06/29/2015] [Accepted: 07/01/2015] [Indexed: 01/01/2023]
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Dargent D, Zins EL, Madebène B, Alikhani ME. Topological insights into the 1/1 diacetyl/water complex gained using a new methodological approach. J Mol Model 2015. [PMID: 26224601 DOI: 10.1007/s00894-015-2751-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The 1/1 diacetyl/water complex is of atmospheric relevance. Previous experimental and theoretical studies have focused on two isomeric forms, and geometry optimizations were carried out on them. Herein, we propose a six-step methodological approach based on topological properties to search for and characterize all of the isomeric forms of the 1/1 noncovalent diacetyl/water complex: (1) a molecular electrostatic potential (MESP) study to get an overview of the V min and V max regions on the molecular surfaces of the separate molecules (diacetyl and water); (2) a topological (QTAIM and ELF) study allowing thorough characterization of the electron densities (QTAIM) and irreducible ELF basins of the separate molecules; (3) full optimization of the predicted structures based on the interaction between complementary reaction sites; (4) energetic characterization based on a symmetry-adapted perturbation theory (SAPT) analysis; (5) topological characterization of the optimized complexes; (6) analysis of the complexes in terms of orbital overlaps (natural bond orbitals, NBO analysis). Using this approach, in addition to achieving the topological characterization of the two isomeric forms already reported, a third possible isomer was identified and characterized. Graphical Abstract Topological tools to study monohydrated complexes.
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Affiliation(s)
- D Dargent
- Sorbonne Universités, UPMC Univ. Paris 06, MONARIS, UMR 8233, Université Pierre et Marie Curie, Pr. M. Esmaïl Alikhani CC 49, 4 place Jussieu, 75252, Paris, France
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Raghavachari K, Saha A. Accurate Composite and Fragment-Based Quantum Chemical Models for Large Molecules. Chem Rev 2015; 115:5643-77. [PMID: 25849163 DOI: 10.1021/cr500606e] [Citation(s) in RCA: 183] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Krishnan Raghavachari
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Arjun Saha
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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Rusinska-Roszak D. Intramolecular O-H···O═C hydrogen bond energy via the molecular tailoring approach to RAHB structures. J Phys Chem A 2015; 119:3674-87. [PMID: 25785364 DOI: 10.1021/acs.jpca.5b02343] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A method for the calculation of the intramolecular hydrogen bond (HB) energy (EHB) by molecular tailoring approach for hydroxycarbonyl aliphatic compounds has been used for compounds with resonance-assisted hydrogen bonding (RAHB). The intramolecular hydrogen bond energies estimated for 229 structures (of 186 compounds) range from 8.2 to 26.3 kcal/mol and show correlation with the geometry descriptors of hydrogen bonds, with the calculated frequencies as well as with topological parameters obtained from the atoms in molecules (AIM) theory. These correlations differ significantly from obtained formerly for saturated nonenolizable structures and prove the special character of the resonance-assisted hydrogen-bonded systems.
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Affiliation(s)
- Danuta Rusinska-Roszak
- Institute of Chemical Technology and Engineering, Poznan University of Technology, ul. Berdychowo 4, 60-965 Poznan, Poland
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