Dmitry Zakharychev | A.E. Arbuzov Institute of Organic and Physical Chemistry Kazan Scientific Centre Russian Academy of Sciences (original) (raw)
Papers by Dmitry Zakharychev
Journal of Structural Chemistry
Two crystalline diastereomorphs of rac-1-benzyl-3-bromo-5-hydroxy-4-[(4-methylphenyl)sulfanyl]-1,... more Two crystalline diastereomorphs of rac-1-benzyl-3-bromo-5-hydroxy-4-[(4-methylphenyl)sulfanyl]-1,5-dihydro-2Н-pyrrole-2-one are obtained and characterized: the racemic compound (P21/c) and the normal conglomerate (P65, P61). The conglomerate is shown to be more thermodynamically preferred while the racemic compound is a metastable form in the entire temperature range studied. These two modifications are formed as a mixture during routine crystallization from a solution and characterized by a similar density, however, their structures significantly differ in the parameters of hydrogen bonds. A small difference in the free energies of two phases at room temperature, which is found by differential scanning calorimetry, explains the experimental availability of both forms during crystallization from the solution. The formation of a stronger hydrogen bond in the conglomerate crystals, which is detected by X-ray diffraction and solid-state vibrational spectroscopy, may be explained by a more favorable arrangement of donor and acceptor groups of the neighboring molecules in a homochiral helix of the conglomerate as compared with a heterochiral dimer, which is the main motif in crystals of the racemic compound.
An entry from the Cambridge Structural Database, the world's repository for small molecule cr... more An entry from the Cambridge Structural Database, the world's repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
An entry from the Cambridge Structural Database, the world's repository for small molecule cr... more An entry from the Cambridge Structural Database, the world's repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
An entry from the Cambridge Structural Database, the world's repository for small molecule cr... more An entry from the Cambridge Structural Database, the world's repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
An entry from the Cambridge Structural Database, the world's repository for small molecule cr... more An entry from the Cambridge Structural Database, the world's repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
An entry from the Cambridge Structural Database, the world's repository for small molecule cr... more An entry from the Cambridge Structural Database, the world's repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
An entry from the Cambridge Structural Database, the world's repository for small molecule cr... more An entry from the Cambridge Structural Database, the world's repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
An entry from the Cambridge Structural Database, the world's repository for small molecule cr... more An entry from the Cambridge Structural Database, the world's repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
Journal of Molecular Structure, 2021
Abstract Available onlineThe physico-chemical characteristics and crystal structure of newly synt... more Abstract Available onlineThe physico-chemical characteristics and crystal structure of newly synthesized isobornanyl sulfoxides and sulfone are presented. After purification, diastereomeric sulfoxides were obtained in a 2:1 eutectic ratio, which did not allow either separation or enrichment of the mixture. Based on thermochemical data, the form of the phase diagram of the system was reconstructed, showing that diastereomers have significantly different melting points. According to the X-ray data, the same supramolecular open–chain S=O•••H–O synthon is built up in the crystals of diastereomeric sulfoxides. The isobornanyl sulfone crystal is formed in a complex way – two crystallographically independent molecules playing different roles in the formation of H-bonds. The IR spectra of a diastereomeric sulfoxides mixture demonstrate the averaging of the synthon-forming functional groups bands. In a counterbalance, the IR spectrum of isobornanyl sulfone shows a doubling of the key bands of synthon-forming functional groups belonging to homochirally homogeneous but crystallographically nonequivalent molecules. 2020 Elsevier Ltd. All rights reserved.
Crystals, 2021
Two polymorphic forms of a conformationally flexible molecule, 5-[(Diphenylphosphoryl)methyl]-4-(... more Two polymorphic forms of a conformationally flexible molecule, 5-[(Diphenylphosphoryl)methyl]-4-(prop-2-en-1-yl)-2,4-dihydro-3H-1,2,4-triazole-3-thione, were obtained by crystallization and characterized by X-ray diffraction analysis and differential scanning calorimetry. The relative stability of polymorphic forms was estimated with DFT calculations of crystal structures and isolated molecules. It turns out, that in the first more dense polymorph with higher cohesion energy and crystal lattice energy, the molecule adopts an energetically unfavorable conformation, and forms dimers with lower H-bond strength, as compared to the second polymorph. On the other hand, in the second polymorph, the molecule adopts almost the lowest-energy conformation and forms infinite chains via strong H-bonds. The first form that seems to be more thermodynamically stable at room temperature transforms into the second form via two endothermic phase transitions; the apparent irreversibility of the transit...
Crystal Growth & Design, 2017
Spontaneous resolution of chiral 3-(2,3-dimethylphenoxy)propane-1,2-diol under the circumstances ... more Spontaneous resolution of chiral 3-(2,3-dimethylphenoxy)propane-1,2-diol under the circumstances of an unusual diversity of racemic crystalline modifications
Russian Journal of Physical Chemistry A, 1995
Acta Crystallographica Section A Foundations and Advances
Crystals
Spontaneous resolution of Pasteur’s salt was historically the first way to obtain pure enantiomer... more Spontaneous resolution of Pasteur’s salt was historically the first way to obtain pure enantiomers from the racemate. The current increase in interest in the direct racemates resolution during crystallization is largely due to the opened prospects for the industrial application of this approach. The chiral 3-(3,4-dimethylphenoxy) propane-1,2-diol 1 is a synthetic precursor of practically useful amino alcohols, the enantiomers of which exhibit different biological effects. In this work, it was first discovered that racemic diol 1 is prone to spontaneous resolution. However, the crystallization process is complicated by the existence, along with the conglomerate, of two other crystalline forms. Using the differential scanning calorimetry (DSC) approach, methods have been developed to obtain individual metastable phases, and all identified modifications ((R)-1, (R+S)-1, α-rac-1, β-rac-1) were ranked by energy. The IR spectroscopy and powder X-ray diffraction (PXRD) methods demonstrated...
Journal of Structural Chemistry
Two crystalline diastereomorphs of rac-1-benzyl-3-bromo-5-hydroxy-4-[(4-methylphenyl)sulfanyl]-1,... more Two crystalline diastereomorphs of rac-1-benzyl-3-bromo-5-hydroxy-4-[(4-methylphenyl)sulfanyl]-1,5-dihydro-2Н-pyrrole-2-one are obtained and characterized: the racemic compound (P21/c) and the normal conglomerate (P65, P61). The conglomerate is shown to be more thermodynamically preferred while the racemic compound is a metastable form in the entire temperature range studied. These two modifications are formed as a mixture during routine crystallization from a solution and characterized by a similar density, however, their structures significantly differ in the parameters of hydrogen bonds. A small difference in the free energies of two phases at room temperature, which is found by differential scanning calorimetry, explains the experimental availability of both forms during crystallization from the solution. The formation of a stronger hydrogen bond in the conglomerate crystals, which is detected by X-ray diffraction and solid-state vibrational spectroscopy, may be explained by a more favorable arrangement of donor and acceptor groups of the neighboring molecules in a homochiral helix of the conglomerate as compared with a heterochiral dimer, which is the main motif in crystals of the racemic compound.
An entry from the Cambridge Structural Database, the world's repository for small molecule cr... more An entry from the Cambridge Structural Database, the world's repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
An entry from the Cambridge Structural Database, the world's repository for small molecule cr... more An entry from the Cambridge Structural Database, the world's repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
An entry from the Cambridge Structural Database, the world's repository for small molecule cr... more An entry from the Cambridge Structural Database, the world's repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
An entry from the Cambridge Structural Database, the world's repository for small molecule cr... more An entry from the Cambridge Structural Database, the world's repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
An entry from the Cambridge Structural Database, the world's repository for small molecule cr... more An entry from the Cambridge Structural Database, the world's repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
An entry from the Cambridge Structural Database, the world's repository for small molecule cr... more An entry from the Cambridge Structural Database, the world's repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
An entry from the Cambridge Structural Database, the world's repository for small molecule cr... more An entry from the Cambridge Structural Database, the world's repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
Journal of Molecular Structure, 2021
Abstract Available onlineThe physico-chemical characteristics and crystal structure of newly synt... more Abstract Available onlineThe physico-chemical characteristics and crystal structure of newly synthesized isobornanyl sulfoxides and sulfone are presented. After purification, diastereomeric sulfoxides were obtained in a 2:1 eutectic ratio, which did not allow either separation or enrichment of the mixture. Based on thermochemical data, the form of the phase diagram of the system was reconstructed, showing that diastereomers have significantly different melting points. According to the X-ray data, the same supramolecular open–chain S=O•••H–O synthon is built up in the crystals of diastereomeric sulfoxides. The isobornanyl sulfone crystal is formed in a complex way – two crystallographically independent molecules playing different roles in the formation of H-bonds. The IR spectra of a diastereomeric sulfoxides mixture demonstrate the averaging of the synthon-forming functional groups bands. In a counterbalance, the IR spectrum of isobornanyl sulfone shows a doubling of the key bands of synthon-forming functional groups belonging to homochirally homogeneous but crystallographically nonequivalent molecules. 2020 Elsevier Ltd. All rights reserved.
Crystals, 2021
Two polymorphic forms of a conformationally flexible molecule, 5-[(Diphenylphosphoryl)methyl]-4-(... more Two polymorphic forms of a conformationally flexible molecule, 5-[(Diphenylphosphoryl)methyl]-4-(prop-2-en-1-yl)-2,4-dihydro-3H-1,2,4-triazole-3-thione, were obtained by crystallization and characterized by X-ray diffraction analysis and differential scanning calorimetry. The relative stability of polymorphic forms was estimated with DFT calculations of crystal structures and isolated molecules. It turns out, that in the first more dense polymorph with higher cohesion energy and crystal lattice energy, the molecule adopts an energetically unfavorable conformation, and forms dimers with lower H-bond strength, as compared to the second polymorph. On the other hand, in the second polymorph, the molecule adopts almost the lowest-energy conformation and forms infinite chains via strong H-bonds. The first form that seems to be more thermodynamically stable at room temperature transforms into the second form via two endothermic phase transitions; the apparent irreversibility of the transit...
Crystal Growth & Design, 2017
Spontaneous resolution of chiral 3-(2,3-dimethylphenoxy)propane-1,2-diol under the circumstances ... more Spontaneous resolution of chiral 3-(2,3-dimethylphenoxy)propane-1,2-diol under the circumstances of an unusual diversity of racemic crystalline modifications
Russian Journal of Physical Chemistry A, 1995
Acta Crystallographica Section A Foundations and Advances
Crystals
Spontaneous resolution of Pasteur’s salt was historically the first way to obtain pure enantiomer... more Spontaneous resolution of Pasteur’s salt was historically the first way to obtain pure enantiomers from the racemate. The current increase in interest in the direct racemates resolution during crystallization is largely due to the opened prospects for the industrial application of this approach. The chiral 3-(3,4-dimethylphenoxy) propane-1,2-diol 1 is a synthetic precursor of practically useful amino alcohols, the enantiomers of which exhibit different biological effects. In this work, it was first discovered that racemic diol 1 is prone to spontaneous resolution. However, the crystallization process is complicated by the existence, along with the conglomerate, of two other crystalline forms. Using the differential scanning calorimetry (DSC) approach, methods have been developed to obtain individual metastable phases, and all identified modifications ((R)-1, (R+S)-1, α-rac-1, β-rac-1) were ranked by energy. The IR spectroscopy and powder X-ray diffraction (PXRD) methods demonstrated...