1
|
Hill NDD, Lilienthal E, Bender CO, Boeré RT. Accurate Crystal Structures of C 12H 9CN, C 12H 8(CN) 2, and C 16H 11CN Valence Isomers Using Nonspherical Atomic Scattering Factors. J Org Chem 2022; 87:16213-16229. [DOI: 10.1021/acs.joc.2c01706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Nathan D. D. Hill
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Dr. W, Lethbridge, AB, Canada T1K 3M4
- The Canadian Centre for Research in Advanced Fluorine Technologies (C-CRAFT), University of Lethbridge, 4401 University Dr. W, Lethbridge, AB, Canada T1K 3M4
| | - Elaura Lilienthal
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Dr. W, Lethbridge, AB, Canada T1K 3M4
- The Canadian Centre for Research in Advanced Fluorine Technologies (C-CRAFT), University of Lethbridge, 4401 University Dr. W, Lethbridge, AB, Canada T1K 3M4
| | - Christopher O. Bender
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Dr. W, Lethbridge, AB, Canada T1K 3M4
| | - René T. Boeré
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Dr. W, Lethbridge, AB, Canada T1K 3M4
- The Canadian Centre for Research in Advanced Fluorine Technologies (C-CRAFT), University of Lethbridge, 4401 University Dr. W, Lethbridge, AB, Canada T1K 3M4
| |
Collapse
|
2
|
Brovarets’ OO, Muradova A, Hovorun DM. Novel horizons of the conformationally-tautomeric transformations of the G·T base pairs: quantum-mechanical investigation. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2026510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Ol’ha O. Brovarets’
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Alona Muradova
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Dmytro M. Hovorun
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| |
Collapse
|
3
|
Ilyin IY, Mirzaeva IV, Sukhikh TS, Bonegardt DV, Basova TV. STUDY OF THE CORRELATION BETWEEN THE STRUCTURE OF THE [Ir(сod)Cp] COMPLEX AND ITS THERMAL PROPERTIES. J STRUCT CHEM+ 2021. [DOI: 10.1134/s0022476621120064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
4
|
Atomistic mechanisms of the tautomerization of the G·C base pairs through the proton transfer: quantum-chemical survey. J Mol Model 2021; 27:367. [PMID: 34855024 DOI: 10.1007/s00894-021-04988-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 11/23/2021] [Indexed: 10/19/2022]
Abstract
This study is devoted to the investigation of the G·C*tO2(WC)↔G*NH3·C*t(WC), G·C*O2(WC)↔G*NH3·C*(WC) and G*·C*O2(WC)↔G*NH3·C(wWC)↓ tautomerization reactions occurring through the proton transfer, obtained at the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of theory in gas phase under normal conditions ('WC' means base pair in Watson-Crick configuration, T=298.15 K). These reactions lead to the formation of the G*NH3·C*t(WC), G*NH3·C*(WC) and G*NH3·C(wWC)↓ base pairs by the participation of the G*NH3 base with NH3 group. Gibbs free energies of activation for these reactions are 6.43, 11.00 and 1.63 kcal·mol-1, respectively. All of these tautomerization reactions are dipole active. Finally, we believe that these non-dissociative processes, which are tightly connected with the tautomeric transformations of the G·C base pairs, play an outstanding role in supporting of the spatial structure of the DNA and RNA molecules with various functional purposes.
Collapse
|
5
|
Grześkiewicz AM, Stefański T, Kubicki M. Weak Intermolecular Interactions in a Series of Bioactive Oxazoles. Molecules 2021; 26:molecules26103024. [PMID: 34069470 PMCID: PMC8159086 DOI: 10.3390/molecules26103024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/11/2021] [Accepted: 05/14/2021] [Indexed: 11/30/2022] Open
Abstract
The intermolecular interactions in a series of nine similar 4,5-phenyl-oxazoles were studied on the basis of crystal structures determined by X-ray diffraction. The crystal architectures were analyzed for the importance and hierarchies of different, weak intermolecular interactions using three approaches: the geometrical characteristics, topological analysis (for the model based on the transfer of multipolar parameters), and energetics of the molecule–molecule interactions. The geometries of the molecules were quite similar and close to the typical values. The results of the analysis of the interactions suggest that the number of nonspecific interactions is more important than the apparent strength of the specific interactions. The interactions involving covalently bound bromine and divalent sulfur atoms were classified as secondary, they certainly did not define the crystal packing, and they played a minor role in the overall crystal cohesion energies. Incidentally, another method for confirming the degree of isostructurality, according to the topologies of the interactions, is described.
Collapse
|
6
|
Brovarets' OO, Muradova A, Hovorun DM. Novel mechanisms of the conformational transformations of the biologically important G·C nucleobase pairs in Watson–Crick, Hoogsteen and wobble configurations via the mutual rotations of the bases around the intermolecular H-bonds: a QM/QTAIM study. RSC Adv 2021; 11:25700-25730. [PMID: 35478902 PMCID: PMC9036977 DOI: 10.1039/d0ra08702e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 06/09/2021] [Indexed: 01/12/2023] Open
Abstract
It was established conformational transformations of the G·C nucleobase pairs, occurring via the mutual rotation of the G and C bases around the intermolecular H-bonds.
Collapse
Affiliation(s)
- Ol'ha O. Brovarets'
- Department of Molecular and Quantum Biophysics
- Institute of Molecular Biology and Genetics
- National Academy of Sciences of Ukraine
- Kyiv
- Ukraine
| | - Alona Muradova
- Department of Molecular Biotechnology and Bioinformatics
- Institute of High Technologies
- Taras Shevchenko National University of Kyiv
- Kyiv
- Ukraine
| | - Dmytro M. Hovorun
- Department of Molecular and Quantum Biophysics
- Institute of Molecular Biology and Genetics
- National Academy of Sciences of Ukraine
- Kyiv
- Ukraine
| |
Collapse
|
7
|
Prokudina YV, Davydova EI, Virovets A, Stöger B, Peresypkina E, Pomogaeva AV, Timoshkin AY. Structures and Chemical Bonding in Antimony(III) Bromide Complexes with Pyridine. Chemistry 2020; 26:16338-16348. [PMID: 32672367 DOI: 10.1002/chem.202002261] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/13/2020] [Indexed: 12/21/2022]
Abstract
Weakly or "partially" bonded molecules are an important link between the chemical and van der Waals interactions. Molecular structures of six new SbBr3 -Py complexes in the solid state have been determined by single-crystal X-ray diffraction analysis. In all complexes all Sb atoms adopt a pseudo-octahedral coordination geometry which is completed by additional Sb⋅⋅⋅Br contacts shorter than the sum of the van der Waals radii, with Br-Sb⋅⋅⋅Br angles close to 180°. To reveal the nature of Sb-Br and Sb-N interactions, the DFT calculations were performed followed by the analysis of the electrostatic potentials, the orbital interactions and the topological analysis. Based on Natural Bond Orbital (NBO) analysis, the Sb-Br interactions range from the covalent bonds to the pnictogen bonds. A simple structural parameter, non-covalence criterion (NCC) is defined as a ratio of the atom-atom distance to the linear combination of sums of covalent and van der Waals radii. NCC correlates with E(2) values for Sb-N, Sb-Cl and Sb-Br bonds, and appears to be useful criterion for a preliminary evaluation of the bonding situation.
Collapse
Affiliation(s)
- Yana V Prokudina
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya emb. 7/9, 199034, St. Petersburg, Russia
| | - Elena I Davydova
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya emb. 7/9, 199034, St. Petersburg, Russia
| | - Alexander Virovets
- University of Regensburg, Universitaetsstr. 31, 93053, Regensburg, Germany
| | - Berthold Stöger
- X-Ray Center, TU Wien, Getreidemarkt, 9, 1060, Vienna, Austria
| | | | - Anna V Pomogaeva
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya emb. 7/9, 199034, St. Petersburg, Russia
| | - Alexey Y Timoshkin
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya emb. 7/9, 199034, St. Petersburg, Russia
| |
Collapse
|
8
|
Brovarets' OO, Muradova A, Hovorun DM. A Quantum-Mechanical Looking Behind the Scene of the Classic G·C Nucleobase Pairs Tautomerization. Front Chem 2020; 8:574454. [PMID: 33330362 PMCID: PMC7732530 DOI: 10.3389/fchem.2020.574454] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/02/2020] [Indexed: 11/13/2022] Open
Abstract
For the first time, at the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of theory, a comprehensive quantum-mechanical investigation of the physico-chemical mechanism of the tautomeric wobblization of the four biologically-important G·C nucleobase pairs by the participation of the monomers in rare, in particular mutagenic, tautomeric forms (marked with an asterisk) was provided. These novel tautomeric transformations (wobblization or shifting of the bases within the pair) are intrinsically inherent properties of the G·C nucleobase pairs. In this study, we have obtained intriguing results, lying far beyond the existing representations. Thus, it was shown that Löwdin's G*·C*(WC) base pair does not tautomerize according to the wobblization mechanism. Tautomeric wobblization of the G*·C*(rWC) (relative Gibbs free energy ΔG = 0.00/relative electronic energy ΔE = 0.00 kcal·mol-1) ("r"-means the configuration of the base pair in reverse position; "WC"-the classic Watson-Crick configuration) and G*t·C*(H) (ΔG = -0.19/ΔE = 0.29 kcal·mol-1) ("H"-Hoogsteen configuration;"t" denotes the O6H hydroxyl group in the trans position) base pairs are preceded by the stages of the base pairs tautomerization by the single proton transfer (SPT). It was established that the G*t·C*(rH) (ΔG = 2.21/ΔE = 2.81 kcal·mol-1) base pair can be wobbled through two different pathways via the traditional one-stage mechanism through the TSs, which are tight G+·C- ion pairs, stabilized by the participation of only two intermolecular H-bonds. It was found out that the G·C base pair is most likely incorporated into the DNA/RNA double helix with parallel strands in the G*·C*(rWC), G·C*(rwwc), and G*·C(rwwc) ("w"-wobble configuration of the pair) tautomeric forms, which are in rapid tautomeric equilibrium with each other. It was proven that the G*·C*(rWC) nucleobase pair is also in rapid tautomeric equilibrium with the eight tautomeric forms of the so-called Levitt base pair. It was revealed that a few cases of tautomerization via the DPT of the nucleobase pairs by the participation of the C8H group of the guanine had occurred. The biological role of the obtained results was also made apparent.
Collapse
Affiliation(s)
- Ol'ha O. Brovarets'
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Alona Muradova
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Dmytro M. Hovorun
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| |
Collapse
|
9
|
Hudson HR, Tajti Á, Bálint E, Czugler M, Karaghiosoff K, Keglevich G. Microwave-assisted synthesis of α-aminophosphonates with sterically demanding α-aryl substituents. SYNTHETIC COMMUN 2020. [DOI: 10.1080/00397911.2019.1679186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Harry R. Hudson
- Faculty of Life Sciences and Computing, London Metropolitan University, London, UK
| | - Ádám Tajti
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Budapest, Hungary
| | - Erika Bálint
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Budapest, Hungary
| | - Mátyás Czugler
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Budapest, Hungary
| | | | - György Keglevich
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Budapest, Hungary
| |
Collapse
|
10
|
A Hidden Side of the Conformational Mobility of the Quercetin Molecule Caused by the Rotations of the O3H, O5H and O7H Hydroxyl Groups: In Silico Scrupulous Study. Symmetry (Basel) 2020. [DOI: 10.3390/sym12020230] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In this study at the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of quantum-mechanical theory it was explored conformational variety of the isolated quercetin molecule due to the mirror-symmetrical hindered turnings of the O3H, O5H and O7H hydroxyl groups, belonging to the A and C rings, around the exocyclic C–O bonds. These dipole active conformational transformations proceed through the 72 transition states (TSs; C1 point symmetry) with non-orthogonal orientation of the hydroxyl groups relatively the plane of the A or C rings of the molecule (HO7C7C8/HO7C7C6 = ±(89.9–93.3), HO5C5C10 = ±(108.9–114.4) and HO3C3C4 = ±(113.6–118.8 degrees) (here and below signs ‘±’ corresponds to the enantiomers)) with Gibbs free energy barrier of activation ΔΔGTS in the range 3.51–16.17 kcal·mol−1 under the standard conditions (T = 298.1 K and pressure 1 atm): ΔΔGTSO7H (3.51–4.27) < ΔΔGTSO3H (9.04–11.26) < ΔΔGTSO5H (12.34–16.17 kcal mol−1). Conformational dynamics of the O3H and O5H groups is partially controlled by the intramolecular specific interactions O3H…O4, C2′/C6′H…O3, O3H…C2′/C6′, O5H…O4 and O4…O5, which are flexible and cooperative. Dipole-active interconversions of the enantiomers of the non-planar conformers of the quercetin molecule (C1 point symmetry) is realized via the 24 TSs with C1 point symmetry (HO3C3C2C1 = ±(11.0–19.1), HC2′/C6′C1′C2 = ±(0.6–2.9) and C3C2C1′C2′/C3C2C1′C6′ = ±(1.7–9.1) degree; ΔΔGTS = 1.65–5.59 kcal·mol−1), which are stabilized by the participation of the intramolecular C2′/C6′H…O1 and O3H…HC2′/C6′ H-bonds. Investigated conformational rearrangements are rather quick processes, since the time, which is necessary to acquire thermal equilibrium does not exceed 6.5 ns.
Collapse
|
11
|
Singh A, Torubaev Y, Ansari SN, Singh SK, Mobin SM, Mathur P. The borderline: exploring the structural landscape of triptycene in cocrystallization with ferrocene. CrystEngComm 2020. [DOI: 10.1039/c9ce01734h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
When the effective packing of triptycene (TripH)–ferrocene chain oligomers in their cocrystal could not be achieved, we reached a borderline at the structural landscape of TripH, where the packing of TripH molecules reproduces the pattern in the native TripH crystal.
Collapse
Affiliation(s)
- Ajeet Singh
- Discipline of Chemistry
- Indian Institute of Technology Indore
- India
| | - Yury Torubaev
- N.S. Kurnakov Institute of General and Inorganic Chemistry of the Russian Academy of Sciences
- Moscow
- Russia
| | | | - Sandip K. Singh
- Discipline of Chemistry
- Indian Institute of Technology Indore
- India
| | - Shaikh M. Mobin
- Discipline of Chemistry
- Indian Institute of Technology Indore
- India
- Discipline of Metallurgy Engineering and Materials Science
- Indian Institute of Technology Indore
| | - Pradeep Mathur
- Discipline of Chemistry
- Indian Institute of Technology Indore
- India
| |
Collapse
|
12
|
Taylor R. Identifying intermolecular atom⋯atom interactions that are not just bonding but also competitive. CrystEngComm 2020. [DOI: 10.1039/d0ce00270d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This highlight criticises the QTAIM method and discusses algorithms for identifying intermolecular interactions that are both bonding and competitive.
Collapse
Affiliation(s)
- Robin Taylor
- Cambridge Crystallographic Data Centre
- Cambridge CB2 1EZ
- UK
| |
Collapse
|
13
|
Brovarets’ OO, Hovorun DM. A new era of the prototropic tautomerism of the quercetin molecule: A QM/QTAIM computational advances. J Biomol Struct Dyn 2019; 38:4774-4800. [PMID: 31711364 DOI: 10.1080/07391102.2019.1691660] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Ol’ha O. Brovarets’
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Dmytro M. Hovorun
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| |
Collapse
|
14
|
Intermolecular Interactions in Ionic Crystals of Nucleobase Chlorides—Combining Topological Analysis of Electron Densities with Energies of Electrostatic Interactions. CRYSTALS 2019. [DOI: 10.3390/cryst9120668] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Understanding intermolecular interactions in crystals of molecular ions continues to be difficult. On the one hand, the analysis of interactions from the point of view of formal charges of molecules, similarly as it is commonly done for inorganic ionic crystals, should be performed. On the other hand, when various functional groups are present in the crystal, it becomes natural to look at the interactions from the point of view of hydrogen bonding, π…π stacking and many other kinds of non-covalent atom–atom bonding. Often, these two approaches seem to lead to conflicting conclusions. On the basis of experimental charge densities of cytosinium chloride, adeninium chloride hemihydrate, and guanine dichloride crystals, with the help of theoretical simulations, we have deeply analysed intermolecular interactions among protonated nucleobases, chloride anions and water molecules. Here, in the second paper of the series of the two (Kumar et al., 2018, IUCrJ 5, 449–469), we focus on applying the above two approaches to the large set of dimers identified in analysed crystals. To understand electrostatic interactions, we analysed electrostatic interaction energies (Ees) computed directly from molecular charge densities and contrasted them with energies computed only from net molecular charges, or from a sum of electric multipolar moments, to find the charge penetration contribution to Ees. To characterize non-covalent interactions we performed topological analyses of crystal electron densities and estimated their interaction energies (EEML) from properties of intermolecular bond critical points. We show that the overall crystal architecture of the studied compounds is governed by the tight packing principle and strong electrostatic attractions and repulsions between ions. Many ions are oriented to each other in a way to strengthen attractive electrostatic interactions or weaken strong repulsion, but not all of them. Numerous bond critical points and bond paths were found between ions, including nucleobase cations despite their overall repulsive interactions. It is clear there is no correlation between EEML and Ees. However, strong relation between EEML and the charge penetration component of Ees is observed. The relation holds regardless of interaction types or whether or not interacting molecules bear the same or opposite charges. Thus, a charge density-based approach for computing intermolecular interaction energies and the atom–atom approach to analyse non-covalent interactions do complement each other, even in ionic systems.
Collapse
|
15
|
Brovarets' OO, Oliynyk TA, Hovorun DM. Novel Tautomerisation Mechanisms of the Biologically Important Conformers of the Reverse Löwdin, Hoogsteen, and Reverse Hoogsteen G *·C * DNA Base Pairs via Proton Transfer: A Quantum-Mechanical Survey. Front Chem 2019; 7:597. [PMID: 31620420 PMCID: PMC6759773 DOI: 10.3389/fchem.2019.00597] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 08/12/2019] [Indexed: 11/22/2022] Open
Abstract
For the first time, in this study with the use of QM/QTAIM methods we have exhaustively investigated the tautomerization of the biologically-important conformers of the G*·C* DNA base pair-reverse Löwdin G*·C*(rWC), Hoogsteen G*'·C*(H), and reverse Hoogsteen G*'·C*(rH) DNA base pairs-via the single (SPT) or double (DPT) proton transfer along the neighboring intermolecular H-bonds. These tautomeric reactions finally lead to the formation of the novel G· C O 2 * (rWC), G N 2 * · C(rWC), G*'N2·C(rWC), G N 7 * · C(H), and G*'N7·C(rH) DNA base mispairs. Gibbs free energies of activation for these reactions are within the range 3.64-31.65 kcal·mol-1 in vacuum under normal conditions. All TSs are planar structures (Cs symmetry) with a single exception-the essentially non-planar transition state TSG*·C*(rWC)↔G+·C-(rWC) (C1 symmetry). Analysis of the kinetic parameters of the considered tautomerization reactions indicates that in reality only the reverse Hoogsteen G*'·C*(rH) base pair undergoes tautomerization. However, the population of its tautomerised state G*'N7·C(rH) amounts to an insignificant value-2.3·10-17. So, the G*·C*(rWC), G*'·C*(H), and G*'·C*(rH) base pairs possess a permanent tautomeric status, which does not depend on proton mobility along the neighboring H-bonds. The investigated tautomerization processes were analyzed in details by applying the author's unique methodology-sweeps of the main physical and chemical parameters along the intrinsic reaction coordinate (IRC). In general, the obtained data demonstrate the tautomeric mobility and diversity of the G*·C* DNA base pair.
Collapse
Affiliation(s)
- Ol'ha O. Brovarets'
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Department of Pharmacology, Bohomolets National Medical University, Kyiv, Ukraine
| | - Timothy A. Oliynyk
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Dmytro M. Hovorun
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
- Department of Pathophysiology, Bohomolets National Medical University, Kyiv, Ukraine
| |
Collapse
|
16
|
Brovarets’ OO, Hovorun DM. Conformational diversity of the quercetin molecule: a quantum-chemical view. J Biomol Struct Dyn 2019; 38:2817-2836. [DOI: 10.1080/07391102.2019.1656671] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Ol’ha O. Brovarets’
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Dmytro M. Hovorun
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| |
Collapse
|
17
|
Brovarets’ OO, Hovorun DM. Conformational transitions of the quercetin molecule via the rotations of its rings: a comprehensive theoretical study. J Biomol Struct Dyn 2019; 38:2865-2883. [DOI: 10.1080/07391102.2019.1645734] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Ol’ha O. Brovarets’
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Department of Pharmacology, Bohomolets National Medical University, Kyiv, Ukraine
| | - Dmytro M. Hovorun
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
- Department of Pathophysiology, Bohomolets National Medical University, Kyiv, Ukraine
| |
Collapse
|
18
|
Taylor R, Wood PA. A Million Crystal Structures: The Whole Is Greater than the Sum of Its Parts. Chem Rev 2019; 119:9427-9477. [PMID: 31244003 DOI: 10.1021/acs.chemrev.9b00155] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The founding in 1965 of what is now called the Cambridge Structural Database (CSD) has reaped dividends in numerous and diverse areas of chemical research. Each of the million or so crystal structures in the database was solved for its own particular reason, but collected together, the structures can be reused to address a multitude of new problems. In this Review, which is focused mainly on the last 10 years, we chronicle the contribution of the CSD to research into molecular geometries, molecular interactions, and molecular assemblies and demonstrate its value in the design of biologically active molecules and the solid forms in which they are delivered. Its potential in other commercially relevant areas is described, including gas storage and delivery, thin films, and (opto)electronics. The CSD also aids the solution of new crystal structures. Because no scientific instrument is without shortcomings, the limitations of CSD research are assessed. We emphasize the importance of maintaining database quality: notwithstanding the arrival of big data and machine learning, it remains perilous to ignore the principle of garbage in, garbage out. Finally, we explain why the CSD must evolve with the world around it to ensure it remains fit for purpose in the years ahead.
Collapse
Affiliation(s)
- Robin Taylor
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
| | - Peter A Wood
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
| |
Collapse
|
19
|
Abstract
In addition to the underlying basic concepts and early recognition of halogen bonding, this paper reviews the conflicting views that consistently appear in the area of noncovalent interactions and the ability of covalently bonded halogen atoms in molecules to participate in noncovalent interactions that contribute to packing in the solid-state. It may be relatively straightforward to identify Type-II halogen bonding between atoms using the conceptual framework of σ-hole theory, especially when the interaction is linear and is formed between the axial positive region (σ-hole) on the halogen in one monomer and a negative site on a second interacting monomer. A σ-hole is an electron density deficient region on the halogen atom X opposite to the R–X covalent bond, where R is the remainder part of the molecule. However, it is not trivial to do so when secondary interactions are involved as the directionality of the interaction is significantly affected. We show, by providing some specific examples, that halogen bonds do not always follow the strict Type-II topology, and the occurrence of Type-I and -III halogen-centered contacts in crystals is very difficult to predict. In many instances, Type-I halogen-centered contacts appear simultaneously with Type-II halogen bonds. We employed the Independent Gradient Model, a recently proposed electron density approach for probing strong and weak interactions in molecular domains, to show that this is a very useful tool in unraveling the chemistry of halogen-assisted noncovalent interactions, especially in the weak bonding regime. Wherever possible, we have attempted to connect some of these results with those reported previously. Though useful for studying interactions of reasonable strength, IUPAC’s proposed “less than the sum of the van der Waals radii” criterion should not always be assumed as a necessary and sufficient feature to reveal weakly bound interactions, since in many crystals the attractive interaction happens to occur between the midpoint of a bond, or the junction region, and a positive or negative site.
Collapse
|
20
|
Is the Fluorine in Molecules Dispersive? Is Molecular Electrostatic Potential a Valid Property to Explore Fluorine-Centered Non-Covalent Interactions? Molecules 2019; 24:molecules24030379. [PMID: 30678158 PMCID: PMC6384640 DOI: 10.3390/molecules24030379] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 01/15/2019] [Accepted: 01/18/2019] [Indexed: 11/23/2022] Open
Abstract
Can two sites of positive electrostatic potential localized on the outer surfaces of two halogen atoms (and especially fluorine) in different molecular domains attract each other to form a non-covalent engagement? The answer, perhaps counterintuitive, is yes as shown here using the electronic structures and binding energies of the interactions for a series of 22 binary complexes formed between identical or different atomic domains in similar or related halogen-substituted molecules containing fluorine. These were obtained using various computational approaches, including density functional and ab initio first-principles theories with M06-2X, RHF, MP2 and CCSD(T). The physical chemistry of non-covalent bonding interactions in these complexes was explored using both Quantum Theory of Atoms in Molecules and Symmetry Adapted Perturbation Theories. The surface reactivity of the 17 monomers was examined using the Molecular Electrostatic Surface Potential approach. We have demonstrated inter alia that the dispersion term, the significance of which is not always appreciated, which emerges either from an energy decomposition analysis, or from a correlated calculation, plays a structure-determining role, although other contributions arising from electrostatic, exchange-repulsion and polarization effects are also important. The 0.0010 a.u. isodensity envelope, often used for mapping the electrostatic potential is found to provide incorrect information about the complete nature of the surface reactive sites on some of the isolated monomers, and can lead to a misinterpretation of the results obtained.
Collapse
|
21
|
Dash SG, Thakur TS. Cation⋯cation hydrogen bonds in synephrine salts: a typical interaction in an unusual environment. Phys Chem Chem Phys 2019; 21:20647-20660. [DOI: 10.1039/c9cp03164b] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Computational studies of hydrogen-bonded cationic species observed in the synephrine salts point towards the stabilizing nature of hydrogen bonds and highlights their contribution in reducing destabilization caused by coulombic repulsion.
Collapse
Affiliation(s)
- Sibananda G. Dash
- Academy of Scientific and Innovative Research (AcSIR)
- CSIR-Central Drug Research Institute (CSIR-CDRI) campus
- Lucknow 226 031
- India
- Molecular and Structural Biology Division
| | - Tejender S. Thakur
- Academy of Scientific and Innovative Research (AcSIR)
- CSIR-Central Drug Research Institute (CSIR-CDRI) campus
- Lucknow 226 031
- India
- Molecular and Structural Biology Division
| |
Collapse
|
22
|
Brovarets' OO, Tsiupa KS, Dinets A, Hovorun DM. Unexpected Routes of the Mutagenic Tautomerization of the T Nucleobase in the Classical A·T DNA Base Pairs: A QM/QTAIM Comprehensive View. Front Chem 2018; 6:532. [PMID: 30538979 PMCID: PMC6277528 DOI: 10.3389/fchem.2018.00532] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 10/12/2018] [Indexed: 01/24/2023] Open
Abstract
In this paper using quantum-mechanical (QM) calculations in combination with Bader's quantum theory of "Atoms in Molecules" (QTAIM) in the continuum with ε = 1, we have theoretically demonstrated for the first time that revealed recently highly-energetic conformers of the classical A·T DNA base pairs - Watson-Crick [A·T(wWC)], reverse Watson-Crick [A·T(wrWC)], Hoogsteen [A·T(wH)] and reverse Hoogsteen [A·T(wrH)] - act as intermediates of the intrapair mutagenic tautomerization of the T nucleobase owing to the novel tautomerisation pathways: A·T(wWC)↔A·T*(w⊥ WC); A·T(wrWC)↔A·T O 2 * (w⊥ rWC); A·T(wH)↔A·T*(w⊥ H); A·T(wrH)↔A·T O 2 * (w⊥ rH). All of them occur via the transition states as tight ion pairs (A+, protonated by the N6H2 amino group)·(T-, deprotonated by the N3H group) with quasi-orthogonal geometry, which are stabilized by the participation of the strong (A)N6+H···O4-/O2-(T) and (A)N6+H···N3-(T) H-bonds. Established tautomerizations proceed through a two-step mechanism of the protons moving in the opposite directions along the intermolecular H-bonds. Initially, proton moves from the N3H imino group of T to the N6H2 amino group of A and then subsequently from the protonated N6+H3 amino group of A to the O4/O2 oxygen atom of T, leading to the products - A·T*(w⊥ WC), A·T O 2 * (w⊥ rWC), A·T*(w⊥ H), and A·T O 2 * (w⊥ rH), which are substantially non-planar, conformationally-labile complexes. These mispairs are stabilized by the participation of the (A)N6H/N6H'···N3(T) and (T)O2H/O4H···N6(A) H-bonds, for which the pyramidalized amino group of A is their donor and acceptor. The Gibbs free energy of activation of these mutagenic tautomerizations lies in the range of 27.8-29.8 kcal·mol-1 at T = 298.15 K in the continuum with ε = 1.
Collapse
Affiliation(s)
- Ol'ha O. Brovarets'
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Department of Pharmacology, Bogomolets National Medical University, Kyiv, Ukraine
| | - Kostiantyn S. Tsiupa
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Andrii Dinets
- Department of Surgery #4, Bogomolets National Medical University, Kyiv, Ukraine
| | - Dmytro M. Hovorun
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Department of Pathophysiology, Bogomolets National Medical University, Kyiv, Ukraine
| |
Collapse
|
23
|
Alhameedi K, Karton A, Jayatilaka D, Thomas SP. Bond orders for intermolecular interactions in crystals: charge transfer, ionicity and the effect on intramolecular bonds. IUCRJ 2018; 5:635-646. [PMID: 30224966 PMCID: PMC6126646 DOI: 10.1107/s2052252518010758] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 07/24/2018] [Indexed: 05/30/2023]
Abstract
The question of whether intermolecular interactions in crystals originate from localized atom⋯atom interactions or as a result of holistic molecule⋯molecule close packing is a matter of continuing debate. In this context, the newly introduced Roby-Gould bond indices are reported for intermolecular 'σ-hole' interactions, such as halogen bonding and chalcogen bonding, and compared with those for hydrogen bonds. A series of 97 crystal systems exhibiting these interaction motifs obtained from the Cambridge Structural Database (CSD) has been analysed. In contrast with conventional bond-order estimations, the new method separately estimates the ionic and covalent bond indices for atom⋯atom and molecule⋯molecule bond orders, which shed light on the nature of these interactions. A consistent trend in charge transfer from halogen/chalcogen bond-acceptor to bond-donor groups has been found in these intermolecular interaction regions via Hirshfeld atomic partitioning of the electron populations. These results, along with the 'conservation of bond orders' tested in the interaction regions, establish the significant role of localized atom⋯atom interactions in the formation of these intermolecular binding motifs.
Collapse
Affiliation(s)
- Khidhir Alhameedi
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth 6009, Australia
- College of Education for Pure Science, University of Karbala, Karbala, Iraq
| | - Amir Karton
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth 6009, Australia
| | - Dylan Jayatilaka
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth 6009, Australia
| | - Sajesh P. Thomas
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth 6009, Australia
- Centre for Materials Crystallography, Department of Chemistry and iNano, Aarhus University, Langelandsgade 140, Aarhus 8000, Denmark
| |
Collapse
|
24
|
Grabowsky S, Mallow O, Pal R, Pergandé Y, Lork E, Näther C, Beckmann J. Conformational trimorphism of bis(2,6-dimesitylphenyl)ditelluride. Z KRIST-CRYST MATER 2018. [DOI: 10.1515/zkri-2018-2077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Besides the previously known α-form (monoclinic, P21/c, Z=4) of bis(2,6-dimesitylphenyl)ditelluride, two new polymorphic modifications, namely the β-form (monoclinic, P21/c, Z=8) and the γ-form (triclinic, P1̅, Z=2), were obtained serendipitously during chemical reactions. In all three modifications, the individual molecules possess significantly different conformations and bond parameters, such as Te–Te bond lengths, C–Te–Te bond angles, C–Te–Te–C torsion angles and intramolecular Menshutkin interactions, which is also reflected in their non-covalent interactions with adjacent molecules in the crystal lattice via London dispersion and electrostatic forces. The interplay between intermolecular and intramolecular forces in these conformational polymorphs was investigated using quantum chemical calculations, which reveal that the β-form should be thermodynamically stable at absolute zero. In contrast, crystallization experiments and thermoanalytical investigations indicate that the α-form is stable at high temperatures and therefore, both forms might be related by enantiotropism.
Collapse
Affiliation(s)
- Simon Grabowsky
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
| | - Ole Mallow
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
| | - Rumpa Pal
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
| | - Yves Pergandé
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
| | - Enno Lork
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
| | - Christian Näther
- Institut für Anorganische Chemie, Christian-Albrechts-Universität zu Kiel , Max-Eyth-Str. 2 , 24118 Kiel , Germany
| | - Jens Beckmann
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
| |
Collapse
|
25
|
Myburgh D, von Berg S, Dillen J. A comparison of energetic criteria to probe the stabilizing interaction resulting from a bond path between congested atoms. J Comput Chem 2018; 39:2273-2282. [DOI: 10.1002/jcc.25547] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/11/2018] [Accepted: 07/11/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Dirkie Myburgh
- Department of Chemistry and Polymer Science; Stellenbosch University; Private Bag X1, maTieland, Stellenbosch 7600 South Africa
| | - Stuart von Berg
- Department of Chemistry and Polymer Science; Stellenbosch University; Private Bag X1, maTieland, Stellenbosch 7600 South Africa
| | - Jan Dillen
- Department of Chemistry and Polymer Science; Stellenbosch University; Private Bag X1, maTieland, Stellenbosch 7600 South Africa
| |
Collapse
|
26
|
Non-dissociative structural transitions of the Watson-Crick and reverse Watson-Crick А·Т DNA base pairs into the Hoogsteen and reverse Hoogsteen forms. Sci Rep 2018; 8:10371. [PMID: 29991693 PMCID: PMC6039495 DOI: 10.1038/s41598-018-28636-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 06/21/2018] [Indexed: 11/08/2022] Open
Abstract
In this study it was theoretically shown that discovered by us recently (Brovarets' et al., Frontiers in Chemistry, 2018, 6:8; doi: 10.3389/fchem.2018.00008) high-energetical, significantly non-planar (symmetry C1), short-lived wobbled conformers of the classical Watson-Crick А·Т(WC), reverse Watson-Crick А·Т(rWC), Hoogsteen А·Т(Н) and reverse Hoogsteen А·Т(rН) DNA base pairs are the intermediates of their pairwise А∙Т(WC)/А∙Т(rWC) ↔ А∙Т(H)/А∙Т(rH) conformational transformations. These transitions do not require for their realization the energy-consumable anisotropic rotation of the amino group of A around the exocyclic C6-N6 bond. They are controlled by the non-planar transition states with quasi-orthogonal geometry (symmetry C1) joined by the single intermolecular (Т)N3H···N6(А) H-bond (~4 kcal∙mol-1). The Gibbs free energies of activation for these non-dissociative, dipole-active conformational transitions consist 7.33 and 7.81 kcal∙mol-1, accordingly. Quantum-mechanical (QM) calculations in combination with Bader's quantum theory of "Atoms in Molecules" (QTAIM) have been performed at the MP2/aug-cc-pVDZ//B3LYP/6-311++G(d,p) level of QM theory in the continuum with ε = 4 under normal conditions.
Collapse
|
27
|
Brovarets’ OO, Tsiupa KS, Hovorun DM. Novel pathway for mutagenic tautomerization of classical А∙Т DNA base pairs via sequential proton transfer through quasi-orthogonal transition states: A QM/QTAIM investigation. PLoS One 2018; 13:e0199044. [PMID: 29949602 PMCID: PMC6021055 DOI: 10.1371/journal.pone.0199044] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 05/30/2018] [Indexed: 12/13/2022] Open
Abstract
In this paper we have theoretically predicted a novel pathway for the mutagenic tautomerization of the classical A∙T DNA base pairs in the free state, the Watson-Crick A·Т(WC), reverse Watson-Crick A·Т(rWC), Hoogsteen A·Т(H) and reverse Hoogsteen A·Т(rH) pairs, via sequential proton transfer accompanied by a significant change in the mutual orientation of the bases. Quantum-mechanical (QM) calculations were performed at the MP2/aug-cc-pVDZ//B3LYP/6-311++G(d,p) level in vacuum phase, along with Bader's quantum theory of Atoms in Molecules (QTAIM). These processes involve transition states (TSs) with quasi-orthogonal structures (symmetry C1), which are highly polar, tight ion pairs (A-, N6H2-deprotonated)∙(T+, O4/O2-protonated). Gibbs free energies of activation for the A∙T(WC) / A∙T(rWC) ↔ A*∙Т(rwWC) / A*∙Т(wWC) tautomeric transitions (~43.5 kcal∙mol-1) are lower than for the A∙T(H) / A∙T(rH) ↔ A*N7∙Т(rwH) / A*N7∙Т(wH) tautomerisations (~53.0 kcal∙mol-1) (rare tautomers are marked by an asterisk; w-wobble configured tautomerisation products). The (T)N3+H⋯N1-(A), (T)O4+H⋯N1-(A) / (T)N3+H⋯N1-(A) and (T)O2+H⋯N1-(A) H-bonds are found in the transition states TSA-·T+A·T(WC)↔A*·T(rwWC) / TSA-·T+A·T(rWC)↔A*·T(wWC). However, in the transition state TSA-·T+A·Т(H)↔A*N7·T(rwH) / TSA-·T+A·Т(rH)↔A*N7·T(wH), the (T)N3+H⋯N7-(A), (T)O4+H⋯N7-(A) / (T)N3+H⋯N7-(A) and (T)O2+H⋯N7-(A) H-bonds are supplemented by the attractive (T)O4+/O2+⋯N6-(A) van der Waals contacts. It was demonstrated that the products of the tautomerization of the classical A∙T DNA base pairs-A*∙Т(rwWC), A*N7∙Т(rwH) and A*N7∙Т(wH) (symmetry Cs)-further transform via double proton transfer into the energetically favorable wobble A∙T*(rwWC), A∙T*(rwH) and A∙T*O2(wH) base mispairs (symmetry Cs).
Collapse
Affiliation(s)
- Ol’ha O. Brovarets’
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Kostiantyn S. Tsiupa
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Dmytro M. Hovorun
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| |
Collapse
|
28
|
|
29
|
Henoch J, Auch A, Diab F, Eichele K, Schubert H, Sirsch P, Block T, Pöttgen R, Wesemann L. Cyclic Distannene or Bis(stannylene) with a Ferrocenyl Backbone: Synthesis, Structure, and Coordination Chemistry. Inorg Chem 2018; 57:4135-4145. [PMID: 29561607 DOI: 10.1021/acs.inorgchem.8b00317] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
1,1'-Dilithioferrocene was reacted with 2 equiv of isopropyl (Ar*) or methyl (Ar') substituted terphenyl tin(II) chloride. Reaction product 1, carrying the bulkier terphenyl substituent Ar*, displays a bis(stannylene) structure in the solid state without formation of a tin-tin bond. Temperature-dependent solution 119Sn NMR spectroscopy, however, revealed a dynamic interplay between bis(stannylene) (100 °C) and cyclic distannene (-80 °C). In contrast to 1, the less bulky Ar' substituent results in a cyclic distannene 2. On the basis of temperature-dependent 119Sn NMR spectroscopy the Sn-Sn bond of compound 2 was preserved up to 100 °C. Both compounds were further characterized by solid-state 119Sn NMR spectroscopy as well as 119Sn and 57Fe Mössbauer spectroscopy. 1 reacted as a chelating ligand with nickel and palladium complexes [Ni(cod)2] and [Pd(nbe)3] (nbe = norbornene). In the resulting coordination compounds the nonstabilized stannylene acts as a donor as well as an acceptor ligand and shows a dynamic switch from donor to acceptor behavior in the monopalladium complex.
Collapse
Affiliation(s)
- Jessica Henoch
- Institut für Anorganische Chemie , Eberhard-Karls-Universität Tübingen , Auf der Morgenstelle 18 , 72076 Tübingen , Germany
| | - Armin Auch
- Institut für Anorganische Chemie , Eberhard-Karls-Universität Tübingen , Auf der Morgenstelle 18 , 72076 Tübingen , Germany
| | - Fatima Diab
- Institut für Anorganische Chemie , Eberhard-Karls-Universität Tübingen , Auf der Morgenstelle 18 , 72076 Tübingen , Germany
| | - Klaus Eichele
- Institut für Anorganische Chemie , Eberhard-Karls-Universität Tübingen , Auf der Morgenstelle 18 , 72076 Tübingen , Germany
| | - Hartmut Schubert
- Institut für Anorganische Chemie , Eberhard-Karls-Universität Tübingen , Auf der Morgenstelle 18 , 72076 Tübingen , Germany
| | - Peter Sirsch
- Institut für Anorganische Chemie , Eberhard-Karls-Universität Tübingen , Auf der Morgenstelle 18 , 72076 Tübingen , Germany
| | - Theresa Block
- Institut für Anorganische und Analytische Chemie , Universität Münster , Corrensstrasse 30 , D-48149 Münster , Germany
| | - Rainer Pöttgen
- Institut für Anorganische und Analytische Chemie , Universität Münster , Corrensstrasse 30 , D-48149 Münster , Germany
| | - Lars Wesemann
- Institut für Anorganische Chemie , Eberhard-Karls-Universität Tübingen , Auf der Morgenstelle 18 , 72076 Tübingen , Germany
| |
Collapse
|
30
|
Brovarets' OO, Tsiupa KS, Hovorun DM. Surprising Conformers of the Biologically Important A·T DNA Base Pairs: QM/QTAIM Proofs. Front Chem 2018; 6:8. [PMID: 29536003 PMCID: PMC5835050 DOI: 10.3389/fchem.2018.00008] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 01/11/2018] [Indexed: 11/22/2022] Open
Abstract
For the first time novel high-energy conformers-A·T(wWC) (5.36), A·T(wrWC) (5.97), A·T(wH) (5.78), and A·T(wrH) (ΔG = 5.82 kcal·mol-1) (See Graphical Abstract) were revealed for each of the four biologically important A·T DNA base pairs - Watson-Crick A·T(WC), reverse Watson-Crick A·T(rWC), Hoogsteen A·T(H) and reverse Hoogsteen A·T(rH) at the MP2/aug-cc-pVDZ//B3LYP/6-311++G(d,p) level of quantum-mechanical theory in the continuum with ε = 4 under normal conditions. Each of these conformers possesses substantially non-planar wobble (w) structure and is stabilized by the participation of the two anti-parallel N6H/N6H'…O4/O2 and N3H…N6 H-bonds, involving the pyramidalized amino group of the A DNA base as an acceptor and a donor of the H-bonding. The transition states - TSA·T(WC)↔A·T(wWC), TSA·T(rWC)↔A·T(wrWC), TSA·T(H)↔A·T(wH), and TSA·T(rH)↔A·T(wrH), controlling the dipole-active transformations of the conformers from the main plane-symmetric state into the high-energy, significantly non-planar state and vice versa, were localized. They also possess wobble structures similarly to the high-energy conformers and are stabilized by the participation of the N6H/N6H'…O4/O2 and N3H…N6 H-bonds. Discovered conformers of the A·T DNA base pairs are dynamically stable short-lived structures [lifetime τ = (1.4-3.9) ps]. Their possible biological significance and future perspectives have been briefly discussed.
Collapse
Affiliation(s)
- Ol'ha O. Brovarets'
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Kostiantyn S. Tsiupa
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Dmytro M. Hovorun
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| |
Collapse
|
31
|
Brovarets' OO, Tsiupa KS, Hovorun DM. The A·T(rWC)/A·T(H)/A·T(rH) ↔ A·T*(rwWC)/A·T*(wH)/A·T*(rwH) mutagenic tautomerization via sequential proton transfer: a QM/QTAIM study. RSC Adv 2018; 8:13433-13445. [PMID: 35542561 PMCID: PMC9079753 DOI: 10.1039/c8ra01446a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 03/23/2018] [Indexed: 12/14/2022] Open
Abstract
In this study for the first time we have revealed by QM and QTAIM calculations at the MP2/aug-cc-pVDZ//B3LYP/6-311++G(d,p) level of QM theory the novel routes of the mutagenic tautomerization of three biologically important A·T DNA base pairs – reverse Watson–Crick A·T(rWC), Hoogsteen A·T(H) and reverse Hoogsteen A·T(rH) – followed by their rebuilding into the wobble (w) A·T*(rwWC), A·T*(wH) and A·T*(rwH) base mispairs by the participation of the mutagenic tautomers of the DNA bases (denoted by asterisk) and vice versa, thus complementing the physico-chemical property of the canonical A·T(WC) Watson–Crick DNA base pair reported earlier (Brovarets' et al., RSC Adv., 2015, 5, 99594–99605). These non-dissociative tautomeric transformations in the classical A·T(rWC), A·T(H) and A·T(rH) DNA base pairs proceed similarly to the canonical A·T(WC) DNA base pair via the intrapair sequential proton transfer with shifting towards major or minor grooves of DNA followed by further double proton transfer along the intermolecular H-bonds and are controlled by the plane symmetric and highly stable transition states – tight ion pairs formed by the A+ nucleobase, protonated by the N1/N7 nitrogen atoms, and T− nucleobase, deprotonated by the N3H imino group. Comparison of the estimated populations of the tautomerised states (10−21 to 10−14) with similar characteristics for the canonical A·T(WC) DNA base pair (10−8 to 10−7) leads authors to the conclusion, that only a base pair with WC architecture can be a building block of the DNA macromolecule as a genetic material, which is able for the evolutionary self-development. Among all four classical DNA base pairs, only A·T(WC) DNA base pair can ensure the proper rate of the spontaneous point errors of replication in DNA. We discovered tautomeric wobbling of the classical A·T DNA base pairs. This data evidence, that only a base pair with Watson–Crick architecture can be a building block of the DNA macromolecule as a genetic material, which is able for the evolutionary self-development.![]()
Collapse
Affiliation(s)
- Ol'ha O. Brovarets'
- Department of Molecular and Quantum Biophysics
- Institute of Molecular Biology and Genetics
- National Academy of Sciences of Ukraine
- 03680 Kyiv
- Ukraine
| | - Kostiantyn S. Tsiupa
- Department of Molecular and Quantum Biophysics
- Institute of Molecular Biology and Genetics
- National Academy of Sciences of Ukraine
- 03680 Kyiv
- Ukraine
| | - Dmytro M. Hovorun
- Department of Molecular and Quantum Biophysics
- Institute of Molecular Biology and Genetics
- National Academy of Sciences of Ukraine
- 03680 Kyiv
- Ukraine
| |
Collapse
|
32
|
Dey D, Chopra D. Quantitative analysis of solid-state diversity in trifluoromethylated phenylhydrazones. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2017; 73:781-793. [PMID: 28980982 DOI: 10.1107/s2052520617006643] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 05/03/2017] [Indexed: 06/07/2023]
Abstract
The cooperative roles of various structural motifs associated with the presence of different intermolecular interactions in the formation of molecular crystals are investigated in a series of trifluoromethylated phenylhydrazones. Out of the six compounds analysed, two exhibit three-dimensional structural similarities with geometrically equivalent building blocks, while a third exists as two polymorphic forms crystallized from ethanol solutions at low temperature (277 K) and room temperature (298 K), respectively. The compounds were characterized via single-crystal and powder X-ray diffraction techniques and differential scanning calorimetry. In the absence of any strong hydrogen bonding, the supramolecular constructs are primarily stabilized via molecular pairs with a high dispersion-energy contribution, due to the presence of molecular stacking along the molecular backbone along with C-H...π interactions in the solid state, in preference to an electrostatic contribution. The interaction energies for the most stabilizing molecular building blocks are in the range -29 to -43 kJ mol-1. In addition, weak N-H...F, C-H...F and N-H...C interactions and F...F, F...C, F...N and C...N contacts act as secondary motifs, providing additional stability to the crystal packing. The overall molecular arrangements are carefully analysed in terms of their nature and energetics, and the roles of different molecular pairs towards the crystal structure are delineated. A topological study using the quantum theory of atoms in molecules was used to characterize all the atomic interactions in the solid state. It established the presence of (3, -1) bond critical points and the closed-shell nature of all the interactions.
Collapse
Affiliation(s)
- Dhananjay Dey
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhouri, Bhopal-By-Pass Road, Bhopal, Madhya Pradesh 462 066, India
| | - Deepak Chopra
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhouri, Bhopal-By-Pass Road, Bhopal, Madhya Pradesh 462 066, India
| |
Collapse
|
33
|
Wang A, Englert U. N-H...X (X = Cl and Br) hydrogen bonds in three isomorphous 3,5-dichloropyridinium salts. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2017; 73:803-809. [PMID: 28978787 DOI: 10.1107/s2053229617013201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 09/14/2017] [Indexed: 11/10/2022]
Abstract
Specific short contacts are important in crystal engineering. Hydrogen bonds have been particularly successful and together with halogen bonds can be useful for assembling small molecules or ions into crystals. The ionic constituents in the isomorphous 3,5-dichloropyridinium (3,5-diClPy) tetrahalometallates 3,5-dichloropyridinium tetrachloridozincate(II), (C5H4Cl2N)2[ZnCl4] or (3,5-diClPy)2ZnCl4, 3,5-dichloropyridinium tetrabromidozincate(II), (C5H4Cl2N)2[ZnBr4] or (3,5-diClPy)2ZnBr4, and 3,5-dichloropyridinium tetrabromidocobaltate(II), (C5H4Cl2N)2[CoBr4] or (3,5-diClPy)2CoBr4, arrange according to favourable electrostatic interactions. Cations are preferably surrounded by anions and vice versa; rare cation-cation contacts are associated with an antiparallel dipole orientation. N-H...X (X = Cl and Br) hydrogen bonds and X...X halogen bonds compete as closest contacts between neighbouring residues. The former dominate in the title compounds; the four symmetrically independent pyridinium N-H groups in each compound act as donors in charge-assisted hydrogen bonds, with halogen ligands and the tetrahedral metallate anions as acceptors. The M-X coordinative bonds in the latter are significantly longer if the halide ligand is engaged in a classical X...H-N hydrogen bond. In all three solids, triangular halogen-bond interactions are observed. They might contribute to the stabilization of the structures, but even the shortest interhalogen contacts are only slightly shorter than the sum of the van der Waals radii.
Collapse
Affiliation(s)
- Ai Wang
- Institute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1, 52074 Aachen, Germany
| | - Ulli Englert
- Institute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1, 52074 Aachen, Germany
| |
Collapse
|
34
|
Raffo PA, Suárez S, Fantoni AC, Baggio R, Cukiernik FD. Polymorphism of a widely used building block for halogen-bonded assemblies: 1,3,5-trifluoro-2,4,6-triiodobenzene. Acta Crystallogr C Struct Chem 2017; 73:667-673. [PMID: 28872062 DOI: 10.1107/s2053229617011007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/26/2017] [Indexed: 11/10/2022] Open
Abstract
After reporting the structure of a new polymorph of 1,3,5-trifluoro-2,4,6-triiodobenzene (denoted BzF3I3), C6F3I3, (I), which crystallized in the space group P21/c, we perform a comparative analysis with the already reported P21/n polymorph, (II) [Reddy et al. (2006). Chem. Eur. J. 12, 2222-2234]. In polymorph (II), type-II I...I halogen bonds and I...π interactions connect molecules in such a way that a three-dimensional structure is formed; however, the way in which molecules are connected in polymorph (I), through type-II I...I halogen bonds and π-π interactions, gives rise to an exfoldable lamellar structure, which looks less tightly bound than that of (II). In agreement with this structural observation, both the melting point and the melting enthalpy of (I) are lower than those of (II).
Collapse
Affiliation(s)
- Pablo A Raffo
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina
| | - Sebastián Suárez
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina
| | - Adolfo C Fantoni
- Instituto de Física de La Plata, Departamento de Física, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Pcia de Buenos Aires, Argentina
| | - Ricardo Baggio
- Gerencia de Investigación y Aplicaciones, Centro Atómico Constituyentes, Comisión Nacional de Energía Atómica, Buenos Aires, Argentina
| | - Fabio D Cukiernik
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina
| |
Collapse
|
35
|
Mackenzie CF, Spackman PR, Jayatilaka D, Spackman MA. CrystalExplorer model energies and energy frameworks: extension to metal coordination compounds, organic salts, solvates and open-shell systems. IUCRJ 2017; 4:575-587. [PMID: 28932404 PMCID: PMC5600021 DOI: 10.1107/s205225251700848x] [Citation(s) in RCA: 545] [Impact Index Per Article: 77.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 06/07/2017] [Indexed: 05/22/2023]
Abstract
The application domain of accurate and efficient CE-B3LYP and CE-HF model energies for intermolecular interactions in molecular crystals is extended by calibration against density functional results for 1794 molecule/ion pairs extracted from 171 crystal structures. The mean absolute deviation of CE-B3LYP model energies from DFT values is a modest 2.4 kJ mol-1 for pairwise energies that span a range of 3.75 MJ mol-1. The new sets of scale factors determined by fitting to counterpoise-corrected DFT calculations result in minimal changes from previous energy values. Coupled with the use of separate polarizabilities for interactions involving monatomic ions, these model energies can now be applied with confidence to a vast number of molecular crystals. Energy frameworks have been enhanced to represent the destabilizing interactions that are important for molecules with large dipole moments and organic salts. Applications to a variety of molecular crystals are presented in detail to highlight the utility and promise of these tools.
Collapse
Affiliation(s)
- Campbell F. Mackenzie
- School of Molecular Sciences, University of Western Australia, Perth, 6009, Australia
| | - Peter R. Spackman
- School of Molecular Sciences, University of Western Australia, Perth, 6009, Australia
| | - Dylan Jayatilaka
- School of Molecular Sciences, University of Western Australia, Perth, 6009, Australia
| | - Mark A. Spackman
- School of Molecular Sciences, University of Western Australia, Perth, 6009, Australia
| |
Collapse
|
36
|
Dittrich B. Is there a future for topological analysis in experimental charge-density research? ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS 2017; 73:325-329. [DOI: 10.1107/s2052520617006680] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 05/03/2017] [Indexed: 11/11/2022]
Abstract
Topological analysis using Bader and co-worker'sAtoms in Moleculestheory has seen many applications in theoretical chemistry and experimental charge-density research. A brief overview of successful early developments, establishing topological analysis as a research tool for characterizing intramolecular chemical bonding, is provided. A lack of vision in many `descriptive but not predictive' subsequent studies is discussed. Limitations of topology for providing accurate energetic estimates of intermolecular interaction energies are put into perspective. It is recommended that topological analyses of well understood bonding situations are phased out and are only reported for unusual bonding. Descriptive studies of intermolecular interactions should have a clear research focus.
Collapse
|
37
|
Piltan M, Farshadfar K, Roe SM. Halogen Bonds Involved in Copper(I) Complexes: A Study Based on the Electronic Charge Density. Eur J Inorg Chem 2017. [DOI: 10.1002/ejic.201700369] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Mohammad Piltan
- Department of Chemistry Faculty of Science, Sanandaj Branch Islamic Azad University Sanandaj Iran
| | - Kaveh Farshadfar
- Department of Chemistry Faculty of Science, Sanandaj Branch Islamic Azad University Sanandaj Iran
| | - S. Mark Roe
- Department of Chemistry School of Life Sciences University of Sussex BN1 9QJ Brighton UK
| |
Collapse
|
38
|
Ilie A, Crespo O, Gimeno MC, Holthausen MC, Laguna A, Diefenbach M, Silvestru C. (N,Se) and (Se,N,Se) Ligands Based on Carborane and Pyridine Fragments - Reactivity of 2,6-[(1′-Me-1′,2′-closo-C2B10H10)SeCH2]2C5H3N towards Copper and Silver. Eur J Inorg Chem 2017. [DOI: 10.1002/ejic.201700075] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Adriana Ilie
- Departamentul de Chimie; Centrul de Chimie Supramoleculară Organică şi Organometalică (CCSOOM); Facultatea de Chimie şi Inginerie Chimică; Universitatea Babeş-Bolyai; 400028 Cluj-Napoca Romania
| | - Olga Crespo
- Departamento de Química Inorgánica; Instituto de Síntesis Química y Catálisis Homogénea (ISQCH); Universidad de Zaragoza-CSIC; 50009 Zaragoza Spain
| | - M. Concepción Gimeno
- Departamento de Química Inorgánica; Instituto de Síntesis Química y Catálisis Homogénea (ISQCH); Universidad de Zaragoza-CSIC; 50009 Zaragoza Spain
| | - Max C. Holthausen
- Institut für Anorganische und Analytische Chemie; Goethe-Universität Frankfurt am Main; Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
| | - Antonio Laguna
- Departamento de Química Inorgánica; Instituto de Síntesis Química y Catálisis Homogénea (ISQCH); Universidad de Zaragoza-CSIC; 50009 Zaragoza Spain
| | - Martin Diefenbach
- Institut für Anorganische und Analytische Chemie; Goethe-Universität Frankfurt am Main; Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
| | - Cristian Silvestru
- Departamentul de Chimie; Centrul de Chimie Supramoleculară Organică şi Organometalică (CCSOOM); Facultatea de Chimie şi Inginerie Chimică; Universitatea Babeş-Bolyai; 400028 Cluj-Napoca Romania
| |
Collapse
|
39
|
Deringer VL, George J, Dronskowski R, Englert U. Plane-Wave Density Functional Theory Meets Molecular Crystals: Thermal Ellipsoids and Intermolecular Interactions. Acc Chem Res 2017; 50:1231-1239. [PMID: 28467707 DOI: 10.1021/acs.accounts.7b00067] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Molecular compounds, organic and inorganic, crystallize in diverse and complex structures. They continue to inspire synthetic efforts and "crystal engineering", with implications ranging from fundamental questions to pharmaceutical research. The structural complexity of molecular solids is linked with diverse intermolecular interactions: hydrogen bonding with all its facets, halogen bonding, and other secondary bonding mechanisms of recent interest (and debate). Today, high-resolution diffraction experiments allow unprecedented insight into the structures of molecular crystals. Despite their usefulness, however, these experiments also face problems: hydrogen atoms are challenging to locate, and thermal effects may complicate matters. Moreover, even if the structure of a crystal is precisely known, this does not yet reveal the nature and strength of the intermolecular forces that hold it together. In this Account, we show that periodic plane-wave-based density functional theory (DFT) can be a useful, and sometimes unexpected, complement to molecular crystallography. Initially developed in the solid-state physics communities to treat inorganic solids, periodic DFT can be applied to molecular crystals just as well: theoretical structural optimizations "help out" by accurately localizing the elusive hydrogen atoms, reaching neutron-diffraction quality with much less expensive measurement equipment. In addition, phonon computations, again developed by physicists, can quantify the thermal motion of atoms and thus predict anisotropic displacement parameters and ORTEP ellipsoids "from scratch". But the synergy between experiment and theory goes much further than that. Once a structure has been accurately determined, computations give new and detailed insights into the aforementioned intermolecular interactions. For example, it has been debated whether short hydrogen bonds in solids have covalent character, and we have added a new twist to this discussion using an orbital-based theory that once more had been developed for inorganic solids. However, there is more to a crystal structure than a handful of short contacts between neighboring residues. We hence have used dimensionally resolved analyses to dissect crystalline networks in a systematic fashion, one spatial direction at a time. Initially applied to hydrogen bonding, these techniques can be seamlessly extended to halogen, chalcogen, and pnictogen bonding, quantifying bond strength and cooperativity in truly infinite networks. Finally, these methods promise to be useful for (bio)polymers, as we have recently exemplified for α-chitin. At the interface of increasingly accurate and popular DFT methods, ever-improving crystallographic expertise, and new challenging, chemical questions, we believe that combined experimental and theoretical studies of molecular crystals are just beginning to pick up speed.
Collapse
Affiliation(s)
- Volker L. Deringer
- Institute
of Inorganic Chemistry and ‡Jülich−Aachen Research
Alliance (JARA-HPC), RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
| | - Janine George
- Institute
of Inorganic Chemistry and ‡Jülich−Aachen Research
Alliance (JARA-HPC), RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
| | - Richard Dronskowski
- Institute
of Inorganic Chemistry and ‡Jülich−Aachen Research
Alliance (JARA-HPC), RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
| | - Ulli Englert
- Institute
of Inorganic Chemistry and ‡Jülich−Aachen Research
Alliance (JARA-HPC), RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
| |
Collapse
|
40
|
Edwards AJ, Mackenzie CF, Spackman PR, Jayatilaka D, Spackman MA. Intermolecular interactions in molecular crystals: what’s in a name? Faraday Discuss 2017; 203:93-112. [DOI: 10.1039/c7fd00072c] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Structure–property relationships are the key to modern crystal engineering, and for molecular crystals this requires both a thorough understanding of intermolecular interactions, and the subsequent use of this to create solids with desired properties. There has been a rapid increase in publications aimed at furthering this understanding, especially the importance of non-canonical interactions such as halogen, chalcogen, pnicogen, and tetrel bonds. Here we show how all of these interactions – and hydrogen bonds – can be readily understood through their common origin in the redistribution of electron density that results from chemical bonding. This redistribution is directly linked to the molecular electrostatic potential, to qualitative concepts such as electrostatic complementarity, and to the calculation of quantitative intermolecular interaction energies. Visualization of these energies, along with their electrostatic and dispersion components, sheds light on the architecture of molecular crystals, in turn providing a link to actual crystal properties.
Collapse
Affiliation(s)
- Alison J. Edwards
- Australian Centre for Neutron Scattering
- Australian Nuclear Science and Technology Organization
- Lucas Heights
- Australia
| | | | - Peter R. Spackman
- School of Molecular Sciences
- University of Western Australia
- Perth
- Australia
| | - Dylan Jayatilaka
- School of Molecular Sciences
- University of Western Australia
- Perth
- Australia
| | - Mark A. Spackman
- School of Molecular Sciences
- University of Western Australia
- Perth
- Australia
| |
Collapse
|
41
|
Granifo J, Arévalo B, Gaviño R, Suárez S, Baggio R. Structural and theoretical characterization of a new twisted 4′-substituted terpyridine compound: 4′-(isoquinolin-4-yl)-2,2′:6′,2′′-terpyridine. Acta Crystallogr C 2016; 72:932-938. [DOI: 10.1107/s2053229616016533] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 10/17/2016] [Indexed: 11/10/2022] Open
Abstract
4′-Substituted derivatives of 2,2′:6′,2′′-terpyridine with N-containing heteroaromatic substituents, such as pyridyl groups, might be able to coordinate metal centres through the extra N-donor atom, in addition to the chelating terpyridine N atoms. The incorporation of these peripheral N-donor sites would also allow for the diversification of the types of noncovalent interactions present, such as hydrogen bonding and π–π stacking. The title compound, C24H16N4, consists of a 2,2′:6′,2′′-terpyridine nucleus (tpy), with a pendant isoquinoline group (isq) bound at the central pyridine (py) ring. The tpy nucleus deviates slightly from planarity, with interplanar angles between the lateral and central py rings in the range 2.24 (7)–7.90 (7)°, while the isq group is rotated significantly [by 46.57 (6)°] out of this planar scheme, associated with a short Htpy...Hisqcontact of 2.32 Å. There are no strong noncovalent interactions in the structure, the main ones being of the π–π and C—H...π types, giving rise to columnar arrays along [001], further linked by C—H...N hydrogen bonds into a three-dimensional supramolecular structure. An Atoms In Molecules (AIM) analysis of the noncovalent interactions provided illuminating results, and while confirming the bonding character for all those interactions unquestionable from a geometrical point of view, it also provided answers for some cases where geometric parameters are not informative, in particular, the short Htpy...Hisqcontact of 2.32 Å to which AIM ascribed an attractive character.
Collapse
|
42
|
Keyvani ZA, Shahbazian S, Zahedi M. Tracing the Fingerprint of Chemical Bonds within the Electron Densities of Hydrocarbons: A Comparative Analysis of the Optimized and the Promolecule Densities. Chemphyschem 2016; 17:3260-3268. [DOI: 10.1002/cphc.201600632] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Zahra Alimohammadi Keyvani
- Faculty of Chemistry, Department of Pure Chemistry; Shahid Beheshti University, G. C.; Tehran 19839 Evin, P.O. Box 19395-4716 Iran), Tel/Fax: (98) 2122-431-661
| | - Shant Shahbazian
- Faculty of Chemistry, Department of Pure Chemistry; Shahid Beheshti University, G. C.; Tehran 19839 Evin, P.O. Box 19395-4716 Iran), Tel/Fax: (98) 2122-431-661
| | - Mansour Zahedi
- Faculty of Chemistry, Department of Pure Chemistry; Shahid Beheshti University, G. C.; Tehran 19839 Evin, P.O. Box 19395-4716 Iran), Tel/Fax: (98) 2122-431-661
| |
Collapse
|
43
|
Brovarets' OO, Hovorun DM. A novel conception for spontaneous transversions caused by homo-pyrimidine DNA mismatches: a QM/QTAIM highlight. Phys Chem Chem Phys 2016. [PMID: 26219928 DOI: 10.1039/c5cp03211c] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We have firstly shown that the T·T(w) and C·C(w) DNA mismatches with wobble (w) geometry stay in slow tautomeric equilibrium with short T·T*(WC) and C·C*(WC) Watson-Crick (WC) mispairs. These non-dissociative tautomeric rearrangements are controlled by the plane-symmetric, highly stable, highly polar and zwitterionic transition states. The obtained results allow us to understand in what way the T·T(w) and C·C(w) mismatches acquire enzymatically competent T·T*(WC) and C·C*(WC) conformations directly in the hydrophobic recognition pocket of a high-fidelity DNA-polymerase, thereby producing thermodynamically non-equilibrium spontaneous transversions. The simplest numerical estimation of the frequency ratio of the TT to CC spontaneous transversions satisfactorily agrees with experimental data.
Collapse
Affiliation(s)
- Ol'ha O Brovarets'
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Akademika Zabolotnoho Str., 03680 Kyiv, Ukraine.
| | | |
Collapse
|
44
|
Dubey R, Mir NA, Desiraju GR. Quaternary cocrystals: combinatorial synthetic strategies based on long-range synthon Aufbau modules (LSAM). IUCRJ 2016; 3:102-7. [PMID: 27006773 PMCID: PMC4775158 DOI: 10.1107/s2052252515023957] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 12/12/2015] [Indexed: 06/01/2023]
Abstract
A synthetic strategy is outlined whereby a binary cocrystal may be developed in turn into a ternary and finally into a quaternary cocrystal. The strategy hinges on the concept of the long-range synthon Aufbau module (LSAM) which is a large supramolecular synthon containing more than one type of intermolecular interaction. Modulation of these interactions may be possible with the use of additional molecular components so that higher level cocrystals are produced. We report six quaternary cocrystals here. All are obtained as nearly exclusive crystallization products when four appropriate solid compounds are taken together in solution for crystallization.
Collapse
Affiliation(s)
- Ritesh Dubey
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Niyaz A. Mir
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Gautam R. Desiraju
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560 012, India
| |
Collapse
|
45
|
Mir NA, Dubey R, Desiraju GR. Four- and five-component molecular solids: crystal engineering strategies based on structural inequivalence. IUCRJ 2016; 3:96-101. [PMID: 27006772 PMCID: PMC4775157 DOI: 10.1107/s2052252515023945] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 12/12/2015] [Indexed: 06/01/2023]
Abstract
A synthetic strategy is described for the co-crystallization of four- and five-component molecular crystals, based on the fact that if any particular chemical constituent of a lower cocrystal is found in two different structural environments, these differences may be exploited to increase the number of components in the solid. 2-Methylresorcinol and tetramethylpyrazine are basic template molecules that allow for further supramolecular homologation. Ten stoichiometric quaternary cocrystals and one quintinary cocrystal with some solid solution character are reported. Cocrystals that do not lend themselves to such homologation are termed synthetic dead ends.
Collapse
Affiliation(s)
- Niyaz A. Mir
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Ritesh Dubey
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Gautam R. Desiraju
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560 012, India
| |
Collapse
|
46
|
Ahmed M, Nassour A, Noureen S, Lecomte C, Jelsch C. Experimental and theoretical charge-density analysis of 1,4-bis(5-hexyl-2-thienyl)butane-1,4-dione: applications of a virtual-atom model. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2016; 72:75-86. [PMID: 26830798 DOI: 10.1107/s2052520615019083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 10/09/2015] [Indexed: 06/05/2023]
Abstract
The experimental and theoretical charge densities of 1,4-bis(5-hexyl-2-thienyl)butane-1,4-dione, a precursor in the synthesis of thiophene-based semiconductors and organic solar cells, are presented. A dummy bond charges spherical atom model is applied besides the multipolar atom model. The results show that the dummy bond charges model is accurate enough to calculate electrostatic-derived properties which are comparable with those obtained by the multipolar atom model. The refinement statistics and the residual electron density values are found to be intermediate between the independent atom and the multipolar formalisms.
Collapse
Affiliation(s)
- Maqsood Ahmed
- Department of Chemistry, The Islamia University of Bahawalpur, 63100, Pakistan
| | - Ayoub Nassour
- Laboratoire de Cristallographie, Résonance Magnétique et Modélisations, CNRS UMR 7036 CRM2, Université de Lorraine, BP 70239, 54506, France
| | - Sajida Noureen
- Department of Chemistry, The Islamia University of Bahawalpur, 63100, Pakistan
| | - Claude Lecomte
- Laboratoire de Cristallographie, Résonance Magnétique et Modélisations, CNRS UMR 7036 CRM2, Université de Lorraine, BP 70239, 54506, France
| | - Christian Jelsch
- Laboratoire de Cristallographie, Résonance Magnétique et Modélisations, CNRS UMR 7036 CRM2, Université de Lorraine, BP 70239, 54506, France
| |
Collapse
|
47
|
Low-melting molecular complexes: Part VII. 2,3-, 2,5- and 3,4-hexanediones and their molecular complexes with chloroform. Struct Chem 2016. [DOI: 10.1007/s11224-015-0620-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
48
|
Abstract
Crystal engineering is discussed, along with its three key concepts: crystal packing; the design of solids; and physical and chemical properties.
Collapse
Affiliation(s)
- Gautam R. Desiraju
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560 012, India
| |
Collapse
|
49
|
Mocilac P, Gallagher JF. Halogenated tennimides and trezimides: impact of halogen bonding and solvent role on porous network formation and inclusion. CrystEngComm 2016. [DOI: 10.1039/c5ce02052b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The role of halogenated and aprotic solvents in macrocyclic structures is assessed in terms of halogen and hydrogen bonding interactions.
Collapse
Affiliation(s)
- P. Mocilac
- School of Chemical Sciences
- Dublin City University
- , Ireland
| | | |
Collapse
|
50
|
Mocilac P, Osman IA, Gallagher JF. Short C–H⋯F interactions involving the 2,5-difluorobenzene group: understanding the role of fluorine in aggregation and complex C–F/C–H disorder in a 2 × 6 isomer grid. CrystEngComm 2016. [DOI: 10.1039/c6ce00795c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|