The Prilezhaev epoxidation of N-Boc-protected 3-cyclobutylidenetropane 1a affords a 1:2 mixture o... more The Prilezhaev epoxidation of N-Boc-protected 3-cyclobutylidenetropane 1a affords a 1:2 mixture of compounds 2a and 2b, in which tropane and cyclobutane fragments are spiro-connected to the oxirane ring in endo- and exo-fashion, respectively. The exo-isomer 2b is obtained in 89% yield and 97% selectivity via the dioxirane oxidation of 1a. BF3-catalyzed isomerization of exo-oxirane 2b results in a 1:1 mixture of the spirocyclic ketones endo 3a and exo 3b containing spiro-connected tropane and cyclopentanone rings, while endo-epoxide 2a gives exclusively endo-ketone 3a. Prilezhaev and dioxirane epoxidations of N-Boc-protected 3-cyclopropylidenetropane 1b affords a mixture of endo- and exo-oxiranes 2c and 2d. Compounds 2c and 2d are not isolated in individual forms since they isomerize into a mixture of spirocyclic ketones endo 3c and exo 3d. Removal of the Boc groups from ketones 3a–d gives the corresponding hydrochlorides of aminoketones 4a–d in quantitative yields. Quantum chemical ...
Abstract An in-depth theoretical analysis of two monosubstituted cyclodextrins (CDs) has been per... more Abstract An in-depth theoretical analysis of two monosubstituted cyclodextrins (CDs) has been performed in order to find the appropriate level of theory capable of the correct qualitative description of their experimentally evidenced self-inclusion phenomenon. The correct increased stability of conformations with substituents included into the cavity (‘IN’ conformations) compared with those in which substituents point outside the cavity (‘OUT’ conformations) is qualitatively predicted by molecular mechanics, the dispersion-corrected self-consistent-charge density-functional tight-binding (SCC-DFTB-D), dispersion-corrected density-functional theory (DFT-D), single-point second-order Moller–Plesset (MP2), and domain based local pair natural orbital coupled cluster (DLPNO-CCSD(T)) computations. The latter four approaches provide also quantitative insights into the relative stability of the ‘IN’ and ‘OUT’ conformations. The method of choice for the fast evaluation of the stability order of the CD conformations is the SCC-DFTB-D that yields relative energies with nearly DFT-D and MP2 accuracy.
ABSTRACT HF and MP2 calculations with the 6-31G** and 6-311G** basis sets and those at MP2/cc-pVT... more ABSTRACT HF and MP2 calculations with the 6-31G** and 6-311G** basis sets and those at MP2/cc-pVTZ level were carried out for the hypothetical tricyclo[2.2.0.01,3]hexane. The results indicate that the molecule under study should have one carbon atom with highly unusual inverted configuration. The analysis of the vibrational frequencies of this molecule as well as the analysis of its plausible decomposition routes performed at the DFT level indicate that this unique molecule could be a plausible synthetic target.
HF and MP2 calculations with the 6-31G∗∗ and 6-311G∗∗ basis sets for the titled molecules and tho... more HF and MP2 calculations with the 6-31G∗∗ and 6-311G∗∗ basis sets for the titled molecules and those at MP2/cc-pVTZ level for the hypothetical tricyclo[3.2.0.01,3]heptane indicate that the latter molecule should have a carbon atom with highly unusual configuration strongly departing from the tetrahedral one. Both analysis of vibrational frequencies of this molecules and comparison of its energy with those of
... Chem. Eur. J. , 7: 24492458. [CrossRef], [PubMed], [Web of Science ®] View all references [6... more ... Chem. Eur. J. , 7: 24492458. [CrossRef], [PubMed], [Web of Science ®] View all references [69]9. Gossage, RA, Jastrzebski, JTBH, van Ameijde, J, Mulders, SJE, Brouwer, AJ, Liskamp, RMJ and van Koten, G. 1999. Tetrahedron Lett. , 40: 14131416. ...
The Diels–Alder reaction of N-benzylcytisine with N-methyl- and N-benzylmaleimides is 100% endo-s... more The Diels–Alder reaction of N-benzylcytisine with N-methyl- and N-benzylmaleimides is 100% endo-selective and gives the corresponding syn- and anti-diastereomers in 11–42% isolated yields. The studies of the reaction progress with LCMS and NMR along with detailed quantum chemical calculations revealed that some Diels–Alder adducts are kinetically and their isomers are thermodynamically controlled products. The Pd/C-catalyzed hydrogenation of benzyl-protected cytisine amine derivatives resulted in the removal of the benzyl group and the addition of hydrogen to the C=C double bond to give the corresponding secondary amines in 45–84% yield. The complete reduction of carbonyl groups in a cytisine derivative with LiAlH4 in THF under reflux afforded the respective tricyclic triamine. Quantum mechanical calculations for the mechanism of the Diels–Alder reaction between the simplest model compounds are presented.
Conformationally restrained exo-isomers of N-Boc-protected spiro[2′,2′-difluorocyclopropane-3′,2′... more Conformationally restrained exo-isomers of N-Boc-protected spiro[2′,2′-difluorocyclopropane-3′,2′-tropanes] were synthesized in 62–83% yield via absolutely diastereoselective cycloaddition of CF2, generated in situ from Me3SiCF3/NaI in refluxing THF, to double bonds of 3-alkylidenetropanes. Standard removal of Boc protecting groups afforded corresponding exo-spiro[2′,2′-difluorocyclopropane-3′,2′-tropane] hydrochlorides in 82–94% yields. DFT and CCSD(T) calculations revealed that the observed exo-selectivity of difluorocarbene addition is likely to be caused by a lower activation barrier of the exo-difluorocyclopropanation compared to the endo-reaction.
We present revised reference values for cell volumes and lattice energies for the widely used X23... more We present revised reference values for cell volumes and lattice energies for the widely used X23 benchmark set of molecular crystals by including the effect of thermal expansion. For this...
Journal of Computational Methods in Sciences and Engineering
Abstract. The present paper focuses on the application of semiempirical quantum molecular dynamic... more Abstract. The present paper focuses on the application of semiempirical quantum molecular dynamics to explore: 1) the reaction dynamics of the elementary reaction Si +(2 P) + H2, which is believed to play a significant role in the growth of thin silicon films, and 2) the dynamics ...
The journal of physical chemistry. A, Jan 21, 2017
We report an alternative quantum mechanical:quantum mechanical (QM:QM) method to the currently us... more We report an alternative quantum mechanical:quantum mechanical (QM:QM) method to the currently used periodic density functional calculations including dispersion and investigate its performance with respect to main structural and energetic properties of the X23 set of molecular crystals. By setting the goal of reproducing reference periodic BLYP+D3 values and by embedding BLYP+D3 into density-functional tight-binding (DFTB), we obtain results similar to those of periodic BLYP+D3 - typically within 1-2% in lattice energies and ~0.4% in cell volumes. The accuracy of this QM:QM method in comparison to DFTB+D and DFT+D for the X23 set of molecular crystals is discussed.
Twenty years have already been passed since the endohedral fullerene's void ceaselessly attra... more Twenty years have already been passed since the endohedral fullerene's void ceaselessly attracts attention of both, experimentalists and theoreticians, computational chemists and physicists in particular, who direct their efforts on computer simulations of encapsulating atoms and molecules into fullerene void and on unraveling the arising bonding patterns. We review recent developments on the endohedral He2 @C60 fullerene, on its experimental observation and on related computational works. The two latter are the main concerns in the present work: on the one hand, there experimentally exists the He dimer embedded into C60 void. On the other, computational side, each He atom exhibits a negligible charge transfer to C60 resulting in that altogether, the He dimer exists as a fractionally charged (He(+)(δ) )2 . Whether there exists a bond between these two helium atoms is the key question of the present work. Since a bond is a two-body creature, we assert that it suffices to define t...
The possible fragmentation pathways of three C2 and three Cs isomers of C82 by unimolecular C2 lo... more The possible fragmentation pathways of three C2 and three Cs isomers of C82 by unimolecular C2 loss were investigated with semi-empirical (PM3), ab initio (HF/STO-3G) and density functional theory (B3LYP/3-21G) calculations. The C2 fragmentation energy of the most stable C2 isomer of C82 calculated with the most reliable model chemistry employed here (B3LYP/3-21G) lies in the 9.1–9.4eV range, which is 0.5–0.9eV larger than the recently reported experimental values. However, other, less stable, isomers were found to have lower fragmentation energies, closer to the experimental data, which suggests that the presence of other isomers in experiments may affect the measured values of the C82 fragmentation energies.
A new self-consistent-charge density-functional tight-binding (SCC-DFTB) set of parameters for Ti... more A new self-consistent-charge density-functional tight-binding (SCC-DFTB) set of parameters for Ti-X pairs of elements (X = Ti, H, C, N, O, S) has been developed. The performance of this set has been tested with respect to TiO2 bulk phases and small molecular systems. It has been found that the band structures, geometric parameters, and cohesive energies of rutile and anatase polymorphs are in good agreement with the reference DFT data and with experiment. Low-index rutile and anatase surfaces were also tested. For molecular systems, binding and atomization energies close to their DFT analogues have been achieved. Large errors, however, have been found for systems in high-spin states and/or having multireference character of their wave functions. The correct performance of SCC-DFTB for surface reactions has been demonstrated via the water splitting on anatase (001) surface. The current SCC-DFTB set is a suitable tool for future in-depth investigation of chemical processes occurring on the surfaces of TiO2 polymorphs as well as for other processes of physicochemical interest.
The C2 fragmentation energies of the most stable isolated-pentagon-rule (IPR) isomers of the C80 ... more The C2 fragmentation energies of the most stable isolated-pentagon-rule (IPR) isomers of the C80 and C82 fullerenes were evaluated with second-order Møller-Plesset (MP2) theory, density-functional theory (DFT) and the semiempirical self-consistent charge density-functional tight-binding (SCC-DFTB) method. Zero-point energy, ionization energy and empirical C2 corrections were included in the calculation of fragmentation energies for comparison with experimental C2 fragmentation energies of the fullerene cations. In the case of the most probable Stone-Wales pathway of C2 fragmentation of C80, the calculated [Formula: see text] agree well with experimental data, whereas in the case of C(82) fragmentation, the calculated [Formula: see text] exceed by up to 1.2 eV the experimental ones, which suggests that other IPR isomers may be present in sufficient amounts in experimental samples. Computer-intensive MP2 calculations and DFT calculations with larger basis sets do not yield much improved C2 fragmentation energies, compared to those reported earlier with B3LYP/3-21G. On the other hand, semiempirical approaches such as SCC-DFTB, which are orders of magnitude less intensive, yield satisfactory fragmentation energies for higher fullerenes and may become a method of choice for routine calculations of fullerenes and carbon nanotubes.
The Prilezhaev epoxidation of N-Boc-protected 3-cyclobutylidenetropane 1a affords a 1:2 mixture o... more The Prilezhaev epoxidation of N-Boc-protected 3-cyclobutylidenetropane 1a affords a 1:2 mixture of compounds 2a and 2b, in which tropane and cyclobutane fragments are spiro-connected to the oxirane ring in endo- and exo-fashion, respectively. The exo-isomer 2b is obtained in 89% yield and 97% selectivity via the dioxirane oxidation of 1a. BF3-catalyzed isomerization of exo-oxirane 2b results in a 1:1 mixture of the spirocyclic ketones endo 3a and exo 3b containing spiro-connected tropane and cyclopentanone rings, while endo-epoxide 2a gives exclusively endo-ketone 3a. Prilezhaev and dioxirane epoxidations of N-Boc-protected 3-cyclopropylidenetropane 1b affords a mixture of endo- and exo-oxiranes 2c and 2d. Compounds 2c and 2d are not isolated in individual forms since they isomerize into a mixture of spirocyclic ketones endo 3c and exo 3d. Removal of the Boc groups from ketones 3a–d gives the corresponding hydrochlorides of aminoketones 4a–d in quantitative yields. Quantum chemical ...
Abstract An in-depth theoretical analysis of two monosubstituted cyclodextrins (CDs) has been per... more Abstract An in-depth theoretical analysis of two monosubstituted cyclodextrins (CDs) has been performed in order to find the appropriate level of theory capable of the correct qualitative description of their experimentally evidenced self-inclusion phenomenon. The correct increased stability of conformations with substituents included into the cavity (‘IN’ conformations) compared with those in which substituents point outside the cavity (‘OUT’ conformations) is qualitatively predicted by molecular mechanics, the dispersion-corrected self-consistent-charge density-functional tight-binding (SCC-DFTB-D), dispersion-corrected density-functional theory (DFT-D), single-point second-order Moller–Plesset (MP2), and domain based local pair natural orbital coupled cluster (DLPNO-CCSD(T)) computations. The latter four approaches provide also quantitative insights into the relative stability of the ‘IN’ and ‘OUT’ conformations. The method of choice for the fast evaluation of the stability order of the CD conformations is the SCC-DFTB-D that yields relative energies with nearly DFT-D and MP2 accuracy.
ABSTRACT HF and MP2 calculations with the 6-31G** and 6-311G** basis sets and those at MP2/cc-pVT... more ABSTRACT HF and MP2 calculations with the 6-31G** and 6-311G** basis sets and those at MP2/cc-pVTZ level were carried out for the hypothetical tricyclo[2.2.0.01,3]hexane. The results indicate that the molecule under study should have one carbon atom with highly unusual inverted configuration. The analysis of the vibrational frequencies of this molecule as well as the analysis of its plausible decomposition routes performed at the DFT level indicate that this unique molecule could be a plausible synthetic target.
HF and MP2 calculations with the 6-31G∗∗ and 6-311G∗∗ basis sets for the titled molecules and tho... more HF and MP2 calculations with the 6-31G∗∗ and 6-311G∗∗ basis sets for the titled molecules and those at MP2/cc-pVTZ level for the hypothetical tricyclo[3.2.0.01,3]heptane indicate that the latter molecule should have a carbon atom with highly unusual configuration strongly departing from the tetrahedral one. Both analysis of vibrational frequencies of this molecules and comparison of its energy with those of
... Chem. Eur. J. , 7: 24492458. [CrossRef], [PubMed], [Web of Science ®] View all references [6... more ... Chem. Eur. J. , 7: 24492458. [CrossRef], [PubMed], [Web of Science ®] View all references [69]9. Gossage, RA, Jastrzebski, JTBH, van Ameijde, J, Mulders, SJE, Brouwer, AJ, Liskamp, RMJ and van Koten, G. 1999. Tetrahedron Lett. , 40: 14131416. ...
The Diels–Alder reaction of N-benzylcytisine with N-methyl- and N-benzylmaleimides is 100% endo-s... more The Diels–Alder reaction of N-benzylcytisine with N-methyl- and N-benzylmaleimides is 100% endo-selective and gives the corresponding syn- and anti-diastereomers in 11–42% isolated yields. The studies of the reaction progress with LCMS and NMR along with detailed quantum chemical calculations revealed that some Diels–Alder adducts are kinetically and their isomers are thermodynamically controlled products. The Pd/C-catalyzed hydrogenation of benzyl-protected cytisine amine derivatives resulted in the removal of the benzyl group and the addition of hydrogen to the C=C double bond to give the corresponding secondary amines in 45–84% yield. The complete reduction of carbonyl groups in a cytisine derivative with LiAlH4 in THF under reflux afforded the respective tricyclic triamine. Quantum mechanical calculations for the mechanism of the Diels–Alder reaction between the simplest model compounds are presented.
Conformationally restrained exo-isomers of N-Boc-protected spiro[2′,2′-difluorocyclopropane-3′,2′... more Conformationally restrained exo-isomers of N-Boc-protected spiro[2′,2′-difluorocyclopropane-3′,2′-tropanes] were synthesized in 62–83% yield via absolutely diastereoselective cycloaddition of CF2, generated in situ from Me3SiCF3/NaI in refluxing THF, to double bonds of 3-alkylidenetropanes. Standard removal of Boc protecting groups afforded corresponding exo-spiro[2′,2′-difluorocyclopropane-3′,2′-tropane] hydrochlorides in 82–94% yields. DFT and CCSD(T) calculations revealed that the observed exo-selectivity of difluorocarbene addition is likely to be caused by a lower activation barrier of the exo-difluorocyclopropanation compared to the endo-reaction.
We present revised reference values for cell volumes and lattice energies for the widely used X23... more We present revised reference values for cell volumes and lattice energies for the widely used X23 benchmark set of molecular crystals by including the effect of thermal expansion. For this...
Journal of Computational Methods in Sciences and Engineering
Abstract. The present paper focuses on the application of semiempirical quantum molecular dynamic... more Abstract. The present paper focuses on the application of semiempirical quantum molecular dynamics to explore: 1) the reaction dynamics of the elementary reaction Si +(2 P) + H2, which is believed to play a significant role in the growth of thin silicon films, and 2) the dynamics ...
The journal of physical chemistry. A, Jan 21, 2017
We report an alternative quantum mechanical:quantum mechanical (QM:QM) method to the currently us... more We report an alternative quantum mechanical:quantum mechanical (QM:QM) method to the currently used periodic density functional calculations including dispersion and investigate its performance with respect to main structural and energetic properties of the X23 set of molecular crystals. By setting the goal of reproducing reference periodic BLYP+D3 values and by embedding BLYP+D3 into density-functional tight-binding (DFTB), we obtain results similar to those of periodic BLYP+D3 - typically within 1-2% in lattice energies and ~0.4% in cell volumes. The accuracy of this QM:QM method in comparison to DFTB+D and DFT+D for the X23 set of molecular crystals is discussed.
Twenty years have already been passed since the endohedral fullerene's void ceaselessly attra... more Twenty years have already been passed since the endohedral fullerene's void ceaselessly attracts attention of both, experimentalists and theoreticians, computational chemists and physicists in particular, who direct their efforts on computer simulations of encapsulating atoms and molecules into fullerene void and on unraveling the arising bonding patterns. We review recent developments on the endohedral He2 @C60 fullerene, on its experimental observation and on related computational works. The two latter are the main concerns in the present work: on the one hand, there experimentally exists the He dimer embedded into C60 void. On the other, computational side, each He atom exhibits a negligible charge transfer to C60 resulting in that altogether, the He dimer exists as a fractionally charged (He(+)(δ) )2 . Whether there exists a bond between these two helium atoms is the key question of the present work. Since a bond is a two-body creature, we assert that it suffices to define t...
The possible fragmentation pathways of three C2 and three Cs isomers of C82 by unimolecular C2 lo... more The possible fragmentation pathways of three C2 and three Cs isomers of C82 by unimolecular C2 loss were investigated with semi-empirical (PM3), ab initio (HF/STO-3G) and density functional theory (B3LYP/3-21G) calculations. The C2 fragmentation energy of the most stable C2 isomer of C82 calculated with the most reliable model chemistry employed here (B3LYP/3-21G) lies in the 9.1–9.4eV range, which is 0.5–0.9eV larger than the recently reported experimental values. However, other, less stable, isomers were found to have lower fragmentation energies, closer to the experimental data, which suggests that the presence of other isomers in experiments may affect the measured values of the C82 fragmentation energies.
A new self-consistent-charge density-functional tight-binding (SCC-DFTB) set of parameters for Ti... more A new self-consistent-charge density-functional tight-binding (SCC-DFTB) set of parameters for Ti-X pairs of elements (X = Ti, H, C, N, O, S) has been developed. The performance of this set has been tested with respect to TiO2 bulk phases and small molecular systems. It has been found that the band structures, geometric parameters, and cohesive energies of rutile and anatase polymorphs are in good agreement with the reference DFT data and with experiment. Low-index rutile and anatase surfaces were also tested. For molecular systems, binding and atomization energies close to their DFT analogues have been achieved. Large errors, however, have been found for systems in high-spin states and/or having multireference character of their wave functions. The correct performance of SCC-DFTB for surface reactions has been demonstrated via the water splitting on anatase (001) surface. The current SCC-DFTB set is a suitable tool for future in-depth investigation of chemical processes occurring on the surfaces of TiO2 polymorphs as well as for other processes of physicochemical interest.
The C2 fragmentation energies of the most stable isolated-pentagon-rule (IPR) isomers of the C80 ... more The C2 fragmentation energies of the most stable isolated-pentagon-rule (IPR) isomers of the C80 and C82 fullerenes were evaluated with second-order Møller-Plesset (MP2) theory, density-functional theory (DFT) and the semiempirical self-consistent charge density-functional tight-binding (SCC-DFTB) method. Zero-point energy, ionization energy and empirical C2 corrections were included in the calculation of fragmentation energies for comparison with experimental C2 fragmentation energies of the fullerene cations. In the case of the most probable Stone-Wales pathway of C2 fragmentation of C80, the calculated [Formula: see text] agree well with experimental data, whereas in the case of C(82) fragmentation, the calculated [Formula: see text] exceed by up to 1.2 eV the experimental ones, which suggests that other IPR isomers may be present in sufficient amounts in experimental samples. Computer-intensive MP2 calculations and DFT calculations with larger basis sets do not yield much improved C2 fragmentation energies, compared to those reported earlier with B3LYP/3-21G. On the other hand, semiempirical approaches such as SCC-DFTB, which are orders of magnitude less intensive, yield satisfactory fragmentation energies for higher fullerenes and may become a method of choice for routine calculations of fullerenes and carbon nanotubes.
Uploads