178 results on '"Roman I. Zubatyuk"'
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2. Crystal structure of 4-tert-butyl-2-{2-[N-(3,3-dimethyl-2-oxobutyl)-N-isopropylcarbamoyl]phenyl}-1-isopropyl-1H-imidazol-3-ium perchlorate
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Olga V. Hordiyenko and Roman I. Zubatyuk
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crystal structure ,α-acylamino ketone ,perchlorate ,disorder ,Crystallography ,QD901-999 - Abstract
In the title salt, C26H40N3O2+·ClO4−, the positive charge of the organic cation is delocalized between the two N atoms of the imidazole ring. The C...;N bond distances are 1.338 (2) and 1.327 (3) Å. The substituents on the benzene ring are rotated almost orthogonal with respect to this ring due to the presence of the bulky isopropyl substituents. The dihedral angle between the benzene and imidazole rings is 75.15 (12)°. Three of the O atoms of the anion are disordered over two sets of sites due to rotation around one of the O—Cl bonds. The ratio of the refined occupancies is 0.591 (14):0.409 (14). In the crystal, the cation and perchlorate anion are bound by an N—H...O hydrogen bond. In addition, the cation–anion pairs are linked into layers parallel to (001) by multiple weak C—H...O hydrogen bonds.
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- 2015
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3. Reactions of α-cyanochalcones with phenylhydrazine
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Maksim A. Kolosov, Valeriy D. Orlov, Nadezhda N. Kolos, Oleg V. Shishkin, and Roman I. Zubatyuk
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Organic chemistry ,QD241-441 - Published
- 2007
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4. Chloridobis(1,10-phenanthroline-κ2N,N′)copper(II) chlorido(1,10-phenanthroline-κ2N,N′)(pyridine-2,6-dicarboxylato-κ3O2,N,O6)manganate(II) methanol monosolvate
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Halyna I. Buvailo, Julia A. Rusanova, Valeriya G. Makhankova, Vladimir N. Kokozay, and Roman I. Zubatyuk
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Crystallography ,QD901-999 - Abstract
The title complex, [CuCl(C12H8N2)2][Mn(C7H3NO4)Cl(C12H8N2)]·CH3OH, consists of discrete [CuCl(phen)2]+ cations (phen is 1,10-phenanthroline), [MnCl(pydc)(phen)]− anions (H2pydc is 2,6-pyridine-2,6-dicarboxylic acid) and one methanol solvent molecule of crystallization per asymmetric unit. It should be noted, that a solvent-masking procedure as implemented in OLEX2 [Dolomanov et al. (2009). J. Appl. Cryst. 42, 339–341] was used to remove the electronic contribution from one disordered solvent molecule, presumably methanol. Only the atoms used in the refined model are reported in chemical formula and related values. The CuII ion is five-coordinated by two phenanthroline ligands and one chloride ion in a distorted trigonal–bipyramidal geometry. The dihedral angle between the phen ligands is 65.21 (5)°. The MnII ion is six-coordinated by one Cl atom, two N atoms from a phen ligand, as well one N atom and two O atoms from pydc in a distorted octahedral coordination geometry, with cis angles ranging from 72.00 (8) to 122.07 (8)° and trans angles ranging from 143.98 (8) to 163.15 (6)°. In the crystal, C—H...O, O—H...O and C—H...Cl hydrogen bonds, cation–anion π–π interactions between the phen ring systems with centroid–centroid distances in the range 3.881 (34)–4.123 (36) Å, as well as cation–cation, anion–anion π–π interactions between the phen rings with centroid–centroid distances in the range 3.763 (4)–3.99 (5) Å and pydc rings with centroid–centroid distances 3.52 (5) Å link the various components.
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- 2014
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5. trans-Chloridobis(ethane-1,2-diamine-κ2N,N′)(thiocyanato-κN)cobalt(III) diamminetetrakis(thiocyanato-κN)cromate(III)
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Julia A. Rusanova, Valentyna V. Semenaka, and Roman I. Zubatyuk
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Crystallography ,QD901-999 - Abstract
The title ionic complex [CoCl(NCS)(C2H8N2)2][Cr(NCS)4(NH3)2], which crystallizes as a non-merohedral twin, is build up of a complex cation [CoCl(NCS)(en)2]+ (en is ethane-1,2-diamine) and the Reinecke's salt anion [Cr(NCS)4(NH3)2]− as complex counter-ion. A network of N—H...S and N—H...Cl hydrogen bonds, as well as short S...S contacts [3.538 (2) and 3.489 (3) Å], between the NCS groups of the complex anions link the molecules into a three-dimentional supramolecular network. Intensity statistic indicated twinning by non-merohedry with refined weighs of twin components are 0.5662:0.4338.
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- 2014
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6. Tris(2,2′-bipyridine)copper(II) pentacyanidonitrosoferrate(II) methanol disolvate monohydrate
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Julia A. Rusanova, Oksana V. Nesterova, Roman I. Zubatyuk, and Olesia V. Kozachuk
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Crystallography ,QD901-999 - Abstract
The title complex [Cu(C10H8N2)3][Fe(CN)5(NO)]·2CH3OH·H2O, consists of discrete [Cu(bpy)3]2+ cations (bpy is 2,2′-bipyridine), [Fe(CN)5NO]2− anions and solvent molecules of crystallization (two methanol molecules and one water molecules per asymmetric unit). The CuII ion adopts a distorted octahedral environment, coordinated by six N atoms from three bpy ligands. The cation charge is balanced by a nitroprusside counter-anion, which has a slightly distorted octahedral coordination geometry. In the crystal, anions and solvent molecules are involved in O—H...N and O—H...O hydrogen bonds, which form chains along [100]. The cations are located between these chains.
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- 2013
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7. Bis(μ-4-nitro-2-{[2-(oxidomethyl)phenyl]iminomethyl}phenolato)bis[chlorido(dimethyl sulfoxide)iron(III)] dimethyl sulfoxide disolvate
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Eduard N. Chygorin, Roman I. Zubatyuk, Oleg V. Shishkin, and Julia A. Rusanova
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Crystallography ,QD901-999 - Abstract
In the centrosymmetric dimeric title complex, [Fe2(C14H10N2O4)2Cl2(C2H6OS)2]·2C2H6OS, two {Fe(L)Cl(DMSO)} units (L is the tridentate ligand 4-nitro-2-{[2-(oxidomethyl)phenyl]iminomethyl}phenolate; DMSO is dimethyl sulfoxide) are bridged by two O atoms, with an Fe...Fe separation of 3.1838 (8) Å. The coordination polyhedron of the FeIII atoms can be described as distorted octahedral, with four Fe—O, one Fe—N and one Fe—Cl coordination bonds. The L ligand is not planar, the dihedral angle between the 2-(oxidomethyl)phenyl]imino and 4-nitro-2-(iminomethyl)phenolate planes being 48.54 (9)°. The solvent DMSO molecule is disordered over two orientations with equal occupancy.
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- 2012
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8. Bis{μ2-2-[(2-hydroxyethyl)(methyl)amino]ethanolato}bis(μ3-N-methyl-2,2′-azanediyldiethanolato)tetrakis(thiocyanatato-κN)dichromium(III)dimanganese(II) dimethylformamide tetrasolvate
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Valentyna V. Semenaka, Oksana V. Nesterova, Volodymyr N. Kokozay, Roman I. Zubatyuk, and Oleg V. Shishkin
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Crystallography ,QD901-999 - Abstract
The heterometallic title complex, [Cr2Mn2(C5H11NO2)2(C5H12NO2)2(NCS)4]·4C3H7NO, was prepared using manganese powder, Reineckes salt, ammonium thiocyanate and a non-aqueous solution of N-methyldiethanolamine in air. The centrosymmetric molecular structure of the complex is based on a tetranuclear {Mn2Cr2(μ-O)6} core. The tetranuclear complex molecule and the two uncoordinated dimethylformamide molecules are linked by O—H...O hydrogen bonds, while the two other molecules of dimethylformamide do not participate in hydrogen bonding.
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- 2011
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9. Bis[N-(2-aminoethyl)ethane-1,2-diamine-κ3N,N′,N′′]copper(II) tris[diamminetetrakis(thiocyanato-κN)chromate(III)] thiocyanate dimethyl sulfoxide tetradecasolvate monohydrate
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Vitalina M. Nikitina, Oksana V. Nesterova, Roman I. Zubatyuk, Oleg V. Shishkin, and Julia A. Rusanova
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Crystallography ,QD901-999 - Abstract
The ionic title complex, [Cu(C4H13N3)2]2[Cr(NCS)4(NH3)2]3(NCS)·14C2H6OS·H2O, consists of complex [Cu(dien)2]2+ cations [dien is N-(2-aminoethyl)ethane-1,2-diamine], complex [Cr(NCS)4(NH3)2]− anions, an NCS− counter-anion and uncoordinated dimethyl sulfoxide (DMSO) and water solvent molecules. One of the Cr atoms lies on an inversion center, while the second Cr atom and the Cu atom lie in general positions. The thiocyanate counter-anion and water molecule are disordered over two positions close to an inversion center. There are several types of hydrogen-bond interactions present in the title compound, which connect the complex cations and anions into bulky [Cu2Cr3] polynuclear species. The four NH3 groups of the complex anions and six bridging DMSO O atoms link the three complex anions via hydrogen bonding into the anionic polynuclear species [Cr(NCS)4(NH3)2]3·6DMSO. The last one is connected by four bridging DMSO O atoms with the two complex copper cations through N—H... O hydrogen bonds between the terminal NH3 groups of the anionic polynuclear species and the NH and NH2 groups of the dien ligand. One additional DMSO molecule is connected via hydrogen bonding to one of the terminal NH3 groups of the anionic polynuclear species. Another DMSO molecule is connected via hydrogen bonding to each Cu(dien)2]2+ cation.
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- 2011
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10. Diaquabis(propane-1,3-diamine)copper(II) bis[diamminetetrakis(thiocyanato-κN)chromate(III)] dimethyl sulfoxide octasolvate
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Vitalina M. Nikitina, Oksana V. Nesterova, Roman I. Zubatyuk, Oleg V. Shishkin, and Julia A. Rusanova
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Crystallography ,QD901-999 - Abstract
The ionic title complex, [Cu(C3H10N2)2(H2O)2][Cr(NCS)4(NH3)2]·8C2H6OS, consists of complex [Cu(dipr)2(H2O)2]2+ copper cations (dipr is propane-1,3-diamine), complex [Cr(NCS)4(NH3)2]− anions and uncoordinated solvent dimethyl sulfoxide (DMSO) molecules. All the metal atoms lie on crystallographic centers of symmetry. The cations are connected to the anions through N—H...O hydrogen bonds between the NH3 molecules of the anion and the water molecules of the cation. The DMSO molecules are involved in hydrogen-bonded linkage of the [Cr(NCS)4(NH3)2]− anions into supramolecular chains through bridging O atoms. A network of hydrogen bonds as well as short S...S contacts [3.5159 (12) and 3.4880 (12) Å] between the NCS groups of the complex anions link the molecules into a three-dimensional supramolecular network.
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- 2011
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11. Ethyl 1,6-dimethyl-2-oxo-4-(quinolin-4-yl)-1,2,3,4-tetrahydropyrimidine-5-carboxylate
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Roman I. Zubatyuk, Oleg V. Shishkin, Heiko Ihmels, Iryna A. Lebedyeva, and Mykhaylo V. Povstyanoy
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Crystallography ,QD901-999 - Abstract
In the title compound, C18H19N3O3, the tetrahydropyrimidone ring adopts a distorted boat conformation. In the crystal structure, intermolecular N—H...O hydrogen bonds link the molecules into centrosymmetric dimers, which are further linked via intermolecular C—H...π interactions. In addition, an intramolecular C—H...O hydrogen bond occurs.
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- 2010
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12. 14-(2,3-Dichlorophenyl)-9,10-dimethylbenzimidazo[1,2-a]benzo[f][1,8]naphthyridine-6-carbonitrile
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Andrii V. Tarasov, Tatyana A. Volovnenko, Roman I. Zubatyuk, Oleg V. Shishkin, and Yulian M. Volovenko
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Crystallography ,QD901-999 - Abstract
In the title compound, C27H16Cl2N4, the benzimidazo[1,2-a]benzo[f][1,8]naphthyridine system is nearly planar (r.m.s. deviation for all non-H atoms = 0.033 Å). The dichlorophenyl substituent is rotated by −67.5 (2)° from this plane. In the crystal structure, molecules form stacks along the crystallographic (100) direction due to π–π stacking interactions with a centroid–centroid distance of 3.4283 (9) Å.
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- 2009
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13. Artificial intelligence-enhanced quantum chemical method with broad applicability
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Roman I. Zubatyuk, Wei Wu, Peikun Zheng, Olexandr Isayev, and Pavlo O. Dral
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Physics ,Multidisciplinary ,Fullerene ,Artificial neural network ,Computer science ,business.industry ,Science ,Method development ,General Physics and Astronomy ,General Chemistry ,General Biochemistry, Genetics and Molecular Biology ,Article ,Quantum chemical method ,Coupled cluster ,Artificial intelligence ,Ground state ,business ,Quantum ,Quantum chemistry - Abstract
High-level quantum mechanical (QM) calculations are indispensable for accurate explanation of natural phenomena on the atomistic level. Their staggering computational cost, however, poses great limitations, which luckily can be lifted to a great extent by exploiting advances in artificial intelligence (AI). Here we introduce the general-purpose, highly transferable artificial intelligence–quantum mechanical method 1 (AIQM1). It approaches the accuracy of the gold-standard coupled cluster QM method with high computational speed of the approximate low-level semiempirical QM methods for the neutral, closed-shell species in the ground state. AIQM1 can provide accurate ground-state energies for diverse organic compounds as well as geometries for even challenging systems such as large conjugated compounds (fullerene C60) close to experiment. This opens an opportunity to investigate chemical compounds with previously unattainable speed and accuracy as we demonstrate by determining geometries of polyyne molecules—the task difficult for both experiment and theory. Noteworthy, our method’s accuracy is also good for ions and excited-state properties, although the neural network part of AIQM1 was never fitted to these properties., Artificial intelligence is combined with quantum mechanics to break the limitations of traditional methods and create a new general-purpose method for computational chemistry simulations with high accuracy, speed and transferability.
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- 2021
14. Effect of Microenvironment on the Geometrical Structure of d(A)5 d(T)5 and d(G)5 d(C)5 DNA Mini-Helixes and the Dickerson Dodecamer: A Density Functional Theory Study
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Dmytro M. Hovorun, Anastasiia Golius, Roman I. Zubatyuk, Leonid Gorb, Tetiana Zubatiuk, Alexey Nyporko, Anatolii Pekh, Mykola M. Ilchenko, Jerzy Leszczynski, and Igor Dubey
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010304 chemical physics ,Chemistry ,Hydrogen bond ,Base pair ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences ,Surfaces, Coatings and Films ,Crystallography ,Dodecameric protein ,Duplex (building) ,0103 physical sciences ,Materials Chemistry ,Density functional theory ,A-DNA ,Physical and Theoretical Chemistry ,Basis set ,Alpha helix - Abstract
We report a comprehensive quantum-chemical study on d(A)5·d(T)5 and d(G)5·d(C)5 DNA mini-helixes and the Dickerson dodecamer d[CGCGAATTCGCG]. The research was performed to model the evolution of the spatial structure of d(A)5·d(T)5 and d(G)5 d(C)5 DNA mini-helixes all the way from vacuum to water bulk. The influence of external factors such as the presence of counterions and the extent of hydration was included. Also, for comparison, limited calculations have been carried out on the Dickerson dodecamer. The study has been performed at the density functional theory level using B97D3 and ωB97XD exchange-correlation functionals augmented by the Def2SVP basis set. We found that the (dA)5·(dT)5 anion when placed in vacuum forms a DNA duplex, which possesses an intermediate form between a helix and a ladder. The presence of compensating Na+ counterions or explicit microhydration of minor and major grooves stabilizes a DNA mini-helix of B-shape. Factors such as water bulk play a minor role. Somewhat different behavior has been found in the case of the (dG)5·(dC)5 duplex. In this case, we observe the formation of B-type mini-helixes even for the (dG)5·(dC)5 anion placed in vacuum. This is due to an additional stabilization originated from the appearance of an extra hydrogen bond, compared to an AT base pair. To assess whether the obtained results are transferable to different sizes of mini-helixes, similar calculations have been performed for the duplex formed by the Dickerson dodecamer which contains a total of 12 dG·dC and dA·dT base pairs. It has been found that in vacuum, analogous to the d(A)5·d(T)5 duplex, this system possesses a shape which is also quite close to a ladder. However, the presence of factors such as hydration restores the B-type geometry. Also, our results completely in line with the results of electrospray-ionization experiments suggest that uncompensated by counterions the DNA backbone preserves the duplex geometry in vacuum. We present arguments that this state is kinetically unstable.
- Published
- 2020
15. Hyperconjugation effect on diene reactivity in 1-methyltetrazolo[5,1-a]isoindole-derived amides and thioamides
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Svitlana V. Shishkina, Roman I. Zubatyuk, Oleg V. Shishkin, Zoia Voitenko, M.D. Tsapko, and Tatyana V. Yegorova
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Diene ,010405 organic chemistry ,Organic Chemistry ,010402 general chemistry ,Hyperconjugation ,01 natural sciences ,Biochemistry ,0104 chemical sciences ,chemistry.chemical_compound ,chemistry ,Computational chemistry ,Amide ,Drug Discovery ,Reactivity (chemistry) ,Isoindole ,Derivative (chemistry) ,Natural bond orbital ,Protic solvent - Abstract
Optimized synthesis of 1-methyltetrazolo[5,1-a]isoindole-derived amides and thioamides was elaborated. Based on 13C NMR spectroscopy and X-Ray diffraction studies data, it was proposed that zwitterionic resonance structures contributed significantly to the structure of these compounds. Geometry optimization was performed in vacuo using m06-2x/cc-pvtz method taking into account polarizing effect of environment (PCM model) and specific intermolecular interactions. Electronic density distribution in these molecules was analyzed using NBO method. Using Δ(HOMOdiene–LUMOdienophile) for amides and thioamides in vacuo and in a protic solvent, possibility of Diels–Alder reaction was evaluated. Energies of π-π conjugation and n→σ* hyperconjugation for the amide derivative were estimated in vacuo, aprotic and protic solvents.
- Published
- 2019
16. Teaching a Neural Network to Attach and Detach Electrons from Molecules
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Olexandr Isayev, Benjamin Nebgen, Sergei Tretiak, Justin S. Smith, and Roman I. Zubatyuk
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Physics ,Computational chemistry ,Multidisciplinary ,Science ,Cheminformatics ,General Physics and Astronomy ,General Chemistry ,Article ,General Biochemistry, Genetics and Molecular Biology ,Electronegativity ,Chemical physics ,Electron affinity ,Ionization ,Physics::Atomic and Molecular Clusters ,Density functional theory ,Physics::Chemical Physics ,Ionization energy ,Quantum chemistry ,Quantum ,Open shell ,Spin-½ - Abstract
Interatomic potentials derived with Machine Learning algorithms such as Deep-Neural Networks (DNNs), achieve the accuracy of high-fidelity quantum mechanical (QM) methods in areas traditionally dominated by empirical force fields and allow performing massive simulations. Most DNN potentials were parametrized for neutral molecules or closed-shell ions due to architectural limitations. In this work, we propose an improved machine learning framework for simulating open-shell anions and cations. We introduce the AIMNet-NSE (Neural Spin Equilibration) architecture, which can predict molecular energies for an arbitrary combination of molecular charge and spin multiplicity with errors of about 2–3 kcal/mol and spin-charges with error errors ~0.01e for small and medium-sized organic molecules, compared to the reference QM simulations. The AIMNet-NSE model allows to fully bypass QM calculations and derive the ionization potential, electron affinity, and conceptual Density Functional Theory quantities like electronegativity, hardness, and condensed Fukui functions. We show that these descriptors, along with learned atomic representations, could be used to model chemical reactivity through an example of regioselectivity in electrophilic aromatic substitution reactions., Quantum mechanical calculations of molecular ionized states are computationally quite expensive. This work reports a successful extension of a previous deep-neural networks approach towards transferable neural-network models for predicting multiple properties of open shell anions and cations.
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- 2021
17. Extending the Applicability of the ANI Deep Learning Molecular Potential to Sulfur and Halogens
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Olexandr Isayev, Kate K. Davis, Christian Devereux, Roman I. Zubatyuk, Kipton Barros, Adrian E. Roitberg, and Justin S. Smith
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Physics ,Speedup ,010304 chemical physics ,Quantum machine learning ,Torsion (mechanics) ,Dihedral angle ,Molecular Dynamics Simulation ,01 natural sciences ,Potential energy ,Computer Science Applications ,Range (mathematics) ,Deep Learning ,Halogens ,0103 physical sciences ,Molecule ,Thermodynamics ,Density functional theory ,Physical and Theoretical Chemistry ,Biological system ,Conformational isomerism ,Quantum ,Density Functional Theory ,Sulfur - Abstract
Machine learning (ML) methods have become powerful, predictive tools in a wide range of applications, such as facial recognition and autonomous vehicles. In the sciences, computational chemists and physicists have been using ML for the prediction of physical phenomena, such as atomistic potential energy surfaces and reaction pathways. Transferable ML potentials, such as ANI-1x, have been developed with the goal of accurately simulating organic molecules containing the chemical elements H, C, N, and O. Here, we provide an extension of the ANI-1x model. The new model, dubbed ANI-2x, is trained to three additional chemical elements: S, F, and Cl. Additionally, ANI-2x underwent torsional refinement training to better predict molecular torsion profiles. These new features open a wide range of new applications within organic chemistry and drug development. These seven elements (H, C, N, O, F, Cl, and S) make up ∼90% of drug-like molecules. To show that these additions do not sacrifice accuracy, we have tested this model across a range of organic molecules and applications, including the COMP6 benchmark, dihedral rotations, conformer scoring, and nonbonded interactions. ANI-2x is shown to accurately predict molecular energies compared to density functional theory with a ∼106 factor speedup and a negligible slowdown compared to ANI-1x and shows subchemical accuracy across most of the COMP6 benchmark. The resulting model is a valuable tool for drug development which can potentially replace both quantum calculations and classical force fields for a myriad of applications.
- Published
- 2020
18. Synthesis and complexation of molecular clips based on diphenylglycoluril and dibenzocrown ethers with alkali metal cations and paraquat
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Alexander Yu. Lyapunov, Roman I. Zubatyuk, Leonid S. Kikot, Tatiana I. Kirichenko, Catherine Yu. Kulygina, Svetlana V. Shishkina, and Tatiana Yu. Bogashchenko
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Bromine ,010405 organic chemistry ,Organic Chemistry ,Stacking ,chemistry.chemical_element ,010402 general chemistry ,Alkali metal ,Cleavage (embryo) ,01 natural sciences ,Biochemistry ,0104 chemical sciences ,chemistry.chemical_compound ,Paraquat ,chemistry ,Hydrogenolysis ,Yield (chemistry) ,Drug Discovery ,Polymer chemistry ,Molecular tweezers - Abstract
A new synthetic route to the molecular clip with diphenylglycoluril and dibenzo-18-crown-6 using protection-deprotection protocol is proposed. Yield of desired compound has increased from 10-15% to 41%. Starting from 4,5-dibromobenzene-1,2-diol 4,5-dibromodibenzo-18-crown-6 and then tetrabromo-substituted molecular clip were obtained. The target molecular clip was obtained by bromine cleavage by hydrogenolysis. Stability constants were determined by spectrophotometric titration with alkali metal cations and paraquat. Quantum-chemical calculations confirm the assumption of additional stabilization of complex with K+ by π–π stacking between the terminal aromatic fragments with formation of a “pseudocryptand” type structure. The structures of complexes of the molecular clips with paraquat were determined by X-ray crystallography.
- Published
- 2018
19. Isotypic Transformation Principle in Molecular Crystals. Analysis of Supramolecular Architecture of Fluorinated Benzenes and Pyridines
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Klaus Merz, Roman I. Zubatyuk, Vera Vasylyeva, and Oleg V. Shishkin
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Materials science ,Supramolecular chemistry ,Solid-state ,Substituent ,chemistry.chemical_element ,Isolobal principle ,02 engineering and technology ,General Chemistry ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Condensed Matter Physics ,Ring (chemistry) ,01 natural sciences ,Transformation (music) ,0104 chemical sciences ,Crystallography ,chemistry.chemical_compound ,chemistry ,Phase (matter) ,Fluorine ,General Materials Science ,0210 nano-technology - Abstract
A systematic topological analysis of fluorinated pyridines and benzenes is reported. Fluorine and nitrogen atoms are considered to be isolobal with respect to the supramolecular architecture in the crystalline phase. The comparison of the intermolecular interaction energies demonstrates that nitrogen atom within the aromatic ring and fluorine as a substituent both induce the same type of molecular arrangement in the solid state. Based on this, we suggest a general isotypic transformation principle for molecular crystals.
- Published
- 2018
20. An alternative approach to the synthesis of 5H-chromeno[4,3-b]pyridin-5-one system using the cleavage of 5H,9H-pyrano[2',3':5,6]chromeno[4,3-b]pyridine-5,9-diones with binucleophiles
- Author
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T. V. Shokol, Oleg V. Shishkin, Oleg A. Lozinski, Roman I. Zubatyuk, and V. P. Khilya
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chemistry.chemical_compound ,chemistry ,010405 organic chemistry ,Stereochemistry ,Organic Chemistry ,Pyridine ,010402 general chemistry ,Ring (chemistry) ,Cleavage (embryo) ,01 natural sciences ,0104 chemical sciences - Abstract
Hantzsch reaction has been successfully employed for a one-step assembling of pyranopyridine fragment to produce 5Н,9Н-pyrano[2',3':5,6]- chromeno[4,3-b]pyridine-5,9-diones which upon treatment with binucleophiles undergo chemoselective γ-pyrone ring opening with the concomitant recyclization to give five-membered cycles, providing a concise route to 6-pyrazolyl(isoxazolyl)-5H-chromeno[4,3-b]- pyridin-5-ones.
- Published
- 2018
21. Complexation of molecular clips containing fragments of diphenylglycoluril and benzocrown ethers with paraquat and its derivatives
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Alexander Yu. Lyapunov, Catherine Yu. Kulygina, Roman I. Zubatyuk, Tatiana I. Kirichenko, Leonid S. Kikot, Tatiana Yu. Bogaschenko, and Svetlana V. Shishkina
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"host–guest chemistry" ,complexation ,crown ethers ,paraquat ,Solid-state ,010402 general chemistry ,01 natural sciences ,Full Research Paper ,lcsh:QD241-441 ,chemistry.chemical_compound ,lcsh:Organic chemistry ,Paraquat ,Polymer chemistry ,molecular clips ,Organic chemistry ,lcsh:Science ,Host–guest chemistry ,Crown ether ,chemistry.chemical_classification ,010405 organic chemistry ,Chemistry ,Organic Chemistry ,0104 chemical sciences ,Ring size ,Diphenylglycoluril ,lcsh:Q ,Molecular tweezers - Abstract
The complexation of molecular clips containing fragments of diphenylglycoluril and benzocrown ethers with paraquat and its derivatives has been studied both in solution and in the solid state. In this paper we studied the influence of the crown ether ring size and the nature of the substituents at the nitrogen atoms of the paraquat derivatives on the composition and stability of these complexes.
- Published
- 2017
22. The ANI-1ccx and ANI-1x data sets, coupled-cluster and density functional theory properties for molecules
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Benjamin Nebgen, Sergei Tretiak, Adrian E. Roitberg, Justin S. Smith, Roman I. Zubatyuk, Nicholas Lubbers, Kipton Barros, and Olexandr Isayev
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Statistics and Probability ,Data Descriptor ,Extrapolation ,Library and Information Sciences ,010402 general chemistry ,01 natural sciences ,Education ,0103 physical sciences ,Statistical physics ,lcsh:Science ,010304 chemical physics ,Dimensionality reduction ,Cheminformatics ,Method development ,Potential energy ,0104 chemical sciences ,Computer Science Applications ,Data set ,Coupled cluster ,Data point ,Density functional theory ,lcsh:Q ,Statistics, Probability and Uncertainty ,Multipole expansion ,Information Systems - Abstract
Maximum diversification of data is a central theme in building generalized and accurate machine learning (ML) models. In chemistry, ML has been used to develop models for predicting molecular properties, for example quantum mechanics (QM) calculated potential energy surfaces and atomic charge models. The ANI-1x and ANI-1ccx ML-based general-purpose potentials for organic molecules were developed through active learning; an automated data diversification process. Here, we describe the ANI-1x and ANI-1ccx data sets. To demonstrate data diversity, we visualize it with a dimensionality reduction scheme, and contrast against existing data sets. The ANI-1x data set contains multiple QM properties from 5 M density functional theory calculations, while the ANI-1ccx data set contains 500 k data points obtained with an accurate CCSD(T)/CBS extrapolation. Approximately 14 million CPU core-hours were expended to generate this data. Multiple QM calculated properties for the chemical elements C, H, N, and O are provided: energies, atomic forces, multipole moments, atomic charges, etc. We provide this data to the community to aid research and development of ML models for chemistry., Measurement(s)Quantum Mechanics • energy • force • multipole moment • atomic chargeTechnology Type(s)computational modeling techniqueFactor Type(s)atomSample Characteristic - Environmentorganic molecule Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.12046440
- Published
- 2019
23. Approaching coupled cluster accuracy with a general-purpose neural network potential through transfer learning
- Author
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Kipton Barros, Benjamin Nebgen, Olexandr Isayev, Nicholas Lubbers, Sergei Tretiak, Christian Devereux, Adrian E. Roitberg, Justin S. Smith, and Roman I. Zubatyuk
- Subjects
0301 basic medicine ,Computational chemistry ,Materials science ,Science ,General Physics and Astronomy ,02 engineering and technology ,010402 general chemistry ,01 natural sciences ,General Biochemistry, Genetics and Molecular Biology ,Article ,Computational science ,Machine Learning ,03 medical and health sciences ,Isomerism ,Thermochemistry ,Computer Simulation ,Physics::Chemical Physics ,lcsh:Science ,Multidisciplinary ,Artificial neural network ,Scale (chemistry) ,General Chemistry ,021001 nanoscience & nanotechnology ,Hydrocarbons ,Chemical space ,0104 chemical sciences ,Benchmarking ,030104 developmental biology ,Coupled cluster ,Physical chemistry ,General purpose ,Scalability ,Thermodynamics ,lcsh:Q ,Neural Networks, Computer ,0210 nano-technology ,Transfer of learning - Abstract
Computational modeling of chemical and biological systems at atomic resolution is a crucial tool in the chemist’s toolset. The use of computer simulations requires a balance between cost and accuracy: quantum-mechanical methods provide high accuracy but are computationally expensive and scale poorly to large systems, while classical force fields are cheap and scalable, but lack transferability to new systems. Machine learning can be used to achieve the best of both approaches. Here we train a general-purpose neural network potential (ANI-1ccx) that approaches CCSD(T)/CBS accuracy on benchmarks for reaction thermochemistry, isomerization, and drug-like molecular torsions. This is achieved by training a network to DFT data then using transfer learning techniques to retrain on a dataset of gold standard QM calculations (CCSD(T)/CBS) that optimally spans chemical space. The resulting potential is broadly applicable to materials science, biology, and chemistry, and billions of times faster than CCSD(T)/CBS calculations., Computational modelling of chemical systems requires a balance between accuracy and computational cost. Here the authors use transfer learning to develop a general purpose neural network potential that approaches quantum-chemical accuracy for reaction thermochemistry, isomerization, and drug-like molecular torsions.
- Published
- 2019
24. The unsubstituted ortho-amidino benzoic acid: crystal structure, characterization and pK a determination
- Author
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Yuliya Yu. Kostina, Oleg V. Shishkin, Angelina V. Biitseva, Olga V. Hordiyenko, Roman I. Zubatyuk, Mikhail Yu. Kornilov, and Ulrich Groth
- Subjects
010405 organic chemistry ,Chemistry ,Hydrogen bond ,Intermolecular force ,Infrared spectroscopy ,Crystal structure ,010402 general chemistry ,Condensed Matter Physics ,01 natural sciences ,Medicinal chemistry ,0104 chemical sciences ,Phthalonitrile ,chemistry.chemical_compound ,Yield (chemistry) ,Zwitterion ,Organic chemistry ,Physical and Theoretical Chemistry ,Benzoic acid - Abstract
The simplest o-amidino benzoic acid—2-(amino(imino)methyl)benzoic acid—has been isolated in 23 % yield as a side product of the reaction of phthalonitrile and ammonia along with desired 1-imino-1H-isoindol-3-amine. This amidino acid was fully characterized by nuclear magnetic resonance, IR spectroscopy, mass spectrometry; pKa values were also determined. X-ray diffraction study and quantum chemical calculations revealed that in the solid state it exists as a zwitterion that is stabilized by intermolecular hydrogen bonds.
- Published
- 2016
25. The synthetic method for 1-(phenyl)alkyl-3-acyl-1,2,8-triazaspiro[4.5]decanes
- Author
-
T. S. Bulda, Roman I. Zubatyuk, L. M. Potikha, Volodymyr O. Kovtunenko, and Oleg V. Shishkin
- Subjects
chemistry.chemical_classification ,chemistry ,Medicinal chemistry ,Alkyl - Abstract
Піперідини, спіросполучені з іншими гетероциклами як структурні елементи фармакологічно активних лейовані фраґменти» лігандів метаботропних рецепторів. Пропонується спосіб отримання похідних 1,2,8-триазаспіро[4.5]декану, який полягає в спіроанелюванні 1,4-дигідропіридинового та піразолонового циклів. При нагріванні 1-(феніл)алкіл-4-[2-[2-арилгідразоно]-1,3-діоксобутил]піридинію галогенідів у піридині або при взаємодії 1-(феніл)алкіл-4-[2-[2-арилгідразоно]-1,3-діоксобутил]піридинію галогенідів і 1-(феніл)алкіл-4-{1,3-діоксо-3-феніл-2-[2-(4-метилфеніл)гідразоно]пропіл}піридинію галогенідів з діізопропілетиламіном при 25оС відбувається внутрішньомолекулярне відновне алкілювання електрофільного піридинієвого катіону з утворенням 1-(феніл)алкіл-3-ацил-1,2,8-триазаспіро[4.5]деканів, які є твердими забарвленими речовинами. Вивчені спектральні властивості продуктів циклізації, на основі яких встановлено утворення спіросполученої системи та присутність фрагменту 1,4-дигідропіридину. Підтвердження їх будови отримане при проведенні РСА кристалу 3-ацетил-8-бензил-1-феніл-1,2,8-триазаспіро[4.5]дека-2,6,9-трієн-4-ону, який однозначно підтвердив ортогональність спіросполучених площин. Дигідропіридиновий цикл у молекулі не є плоским і знаходиться в конформації півкрісло, в якій спіроатом Карбону відхилений від площини інших атомів циклу, що є наслідком утворення внутрішньомолекулярного C-H…π водневого зв’язку.
- Published
- 2016
26. 2018 T Division Lightning Talks
- Author
-
Lampros Svolos, Morgan E. Gorris, Kayla Diann Davie, Jacob Paul Tavenner, Levi Lystrom, D. L. Danielson, Luke Clyde Adams, Katherine Candice Kempfert, Kristin Nicole Mackowski, Brendan Alan Smith, Michael Sakano, Kaitlyn Scheib, Phuong Nguyen Uyen Chau, Jessica Conrad, Siddharth Bhela, Jeannie Marie Leesman, Kenneth C. Sockwell, Sina G. Lewis, Marilyn Leann Ramsey, Barton Jed Brown, Roman I. Zubatyuk, Kaitlyn Martinez, Sabine Silvia Zentgraf, Biswas Rijal, Michael John Gonzales, Bowen Li, Colin Mackenzie Adams, Jamil Gafur, and Lewis R. Baker
- Subjects
Engineering ,Meteorology ,business.industry ,Division (mathematics) ,business ,Lightning - Published
- 2018
27. Accurate and Transferable Multitask Prediction of Chemical Properties with an Atoms-in-Molecule Neural Network
- Author
-
Olexandr Isayev, Roman I. Zubatyuk, Jerzy Leszczynski, and Justin S. Smith
- Subjects
Multidisciplinary ,Artificial neural network ,010304 chemical physics ,Computer science ,Implicit solvation ,Atoms in molecules ,Solvation ,SciAdv r-articles ,Macroscopic quantum phenomena ,010402 general chemistry ,01 natural sciences ,Force field (chemistry) ,0104 chemical sciences ,Chemistry ,010404 medicinal & biomolecular chemistry ,Computer Science ,0103 physical sciences ,Benchmark (computing) ,Median absolute deviation ,Algorithm ,Research Articles ,Research Article - Abstract
We introduce a modular, chemically inspired deep neural network model for prediction of several atomic and molecular properties., Atomic and molecular properties could be evaluated from the fundamental Schrodinger’s equation and therefore represent different modalities of the same quantum phenomena. Here, we present AIMNet, a modular and chemically inspired deep neural network potential. We used AIMNet with multitarget training to learn multiple modalities of the state of the atom in a molecular system. The resulting model shows on several benchmark datasets state-of-the-art accuracy, comparable to the results of orders of magnitude more expensive DFT methods. It can simultaneously predict several atomic and molecular properties without an increase in the computational cost. With AIMNet, we show a new dimension of transferability: the ability to learn new targets using multimodal information from previous training. The model can learn implicit solvation energy (SMD method) using only a fraction of the original training data and an archive median absolute deviation error of 1.1 kcal/mol compared to experimental solvation free energies in the MNSol database.
- Published
- 2018
28. Single-stage synthesis of 3-hydroxy- and 3-alkoxy-5-arylimidazolidine-2,4-diones by reaction of arylglyoxal hydrates with N-hydroxy- and N-alkoxyureas
- Author
-
Vasiliy G. Shtamburg, Svetlana V. Kravchenko, V. V. Shtamburg, Andrey A. Anishchenko, Remir G. Kostyanovsky, Eugene A. Klotz, Roman I. Zubatyuk, and Aleksander V. Mazepa
- Subjects
Acetic acid ,chemistry.chemical_compound ,chemistry ,Single stage ,Organic Chemistry ,Alkoxy group ,Organic chemistry ,N-Hydroxyurea - Abstract
Arylglyoxal hydrates interact with N-alkoxyureas and N-hydroxyurea in acetic acid with selective formation of 3-alkoxy-5-arylimidazolidine-2,4-diones and 5-aryl-3-hydroxyimidazolidine-2,4-diones, respectively. The structures of 3-methoxy-5-phenylimidazolidine-2,4-dione, 3-ethoxy-5-phenylimidazolidine-2,4-dione, and 3-butoxy-5-(4-chlorophenyl)imidazolidine-2,4-dione were studied by X-ray structural analysis.
- Published
- 2015
29. Influence of chlorine substituents on the aggregation behavior of chlorobenzoyl-substituted ferrocene derivates
- Author
-
Marcus Maschke, Klaus Merz, Olel V. Shishkin, Nils Metzler-Nolte, and Roman I. Zubatyuk
- Subjects
010405 organic chemistry ,Chemistry ,Aryl ,Intermolecular force ,Stacking ,Substituent ,Ab initio ,Crystal structure ,010402 general chemistry ,Condensed Matter Physics ,01 natural sciences ,0104 chemical sciences ,Crystal ,chemistry.chemical_compound ,Computational chemistry ,polycyclic compounds ,Molecule ,Physical and Theoretical Chemistry - Abstract
The influence of chlorine substituents on the molecular arrangement in the solid state of chlorinated benzoyl-ferrocene derivates with restricted molecular flexibility was investigated by crystal structure determinations and theoretical calculations. Four different chlorinated benzoyl-ferrocene derivates were crystallized from a saturated CHCl3 solution and analyzed by X-ray diffraction. Under consideration of the structural restrictions, a comparable trend of rearrangement in the crystal organization with increasing number of chlorine atoms is observed, which is analogous to findings for chlorine-substituted benzenes. More important, the molecules arrange in layers (1 and 4) and columns (2 and 3) and in all cases with repulsively orientated CF3···CF3 substituents. In addition, Cl···Cl interactions are visible in 1 (type I) and 4 (type II). Furthermore, the crystal packing motifs were also analyzed based on ab initio quantum-chemical calculations of the intermolecular interaction energy, using the B97-D3/def2-TZVP method. According to the topology of intermolecular interaction, the crystal structures have either columnar or layered structure depending on the presence of Cl substituent in para-position of benzene ring. It was also found that Cl···Cl interactions play a secondary role in crystal organization, and the substituent effect is maybe due to polarization of the aromatic ring, which leads ultimately to an increase in the energy of stacking interactions between the aryl substituents. Analysis of the crystal structures of chlorine substituents on the molecular arrangement in the solid state of restricted molecular flexible chlorinated benzoyl-ferrocene derivates shows a trend of rearrangement in the crystal organization with increasing number of chlorine atoms.
- Published
- 2015
30. Reactions of octahydroacridine-4-carbonitrile (carboxamide) with electrophilic reagents
- Author
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Aleksandr V. Mazepa, Ekaterina V. Zaliznaya, Elena V. Vashchenko, Oleg K. Farat, Viktor I. Markov, Nikolay Yu. Gorobets, and Roman I. Zubatyuk
- Subjects
Substitution reaction ,Chemistry ,medicine.drug_class ,Japp–Klingemann reaction ,Organic Chemistry ,chemistry.chemical_element ,Carboxamide ,Azo coupling ,Nitrogen ,Electrophilic substitution ,Reagent ,Electrophile ,medicine ,Organic chemistry - Abstract
Octahydroacridine-4-carbonitrile (carboxamide) was shown to react with aryldiazonium salts and other electrophilic reagents in acidic and neutral media. The reactions occurred at the methine carbon atom, forming the corresponding 4-functionalized derivatives. The obtained azo compounds decomposed at 140–155°С with elimination of nitrogen and gave products formed by the reactions of radical intermediates.
- Published
- 2015
31. New Fluorenocrownophanes with Naphthalene Fragments: Synthesis, Structure, Properties and Interaction with Paraquat
- Author
-
Irene S. Yakovenko, Alexander V. Lobach, Svetlana V. Shishkina, E. Yu. Kulygina, T. I. Kirichenko, A. Yu. Lyapunov, and Roman I. Zubatyuk
- Subjects
chemistry.chemical_compound ,Paraquat ,chemistry ,Organic Chemistry ,Photochemistry ,Analytical Chemistry ,Naphthalene - Published
- 2015
32. d(A)3d(T)3 and d(G)3d(C)3 B-DNA mini-helixes: the DFT/M06-2x and DFT/B97-D3 comparison of geometrical and energetic characteristics
- Author
-
Tatiana A. Zubatiuk, Leonid Gorb, Jerzy Leszczynski, Dmytro M. Hovorun, and Roman I. Zubatyuk
- Subjects
Basis set superposition error ,Physics ,010304 chemical physics ,Basis (linear algebra) ,Hydrogen bond ,Organic Chemistry ,Thermodynamics ,Type (model theory) ,010402 general chemistry ,01 natural sciences ,Catalysis ,0104 chemical sciences ,Computer Science Applications ,Ion ,Inorganic Chemistry ,Molecular dynamics ,Crystallography ,Computational Theory and Mathematics ,0103 physical sciences ,Counterpoise ,Physical and Theoretical Chemistry ,Basis set - Abstract
We report the comprehensive DFT based comparison of geometrical and energetic parameters of the d(A)3·d(T)3 and d(G)3·d(C)3 nucleic acid mini-helixes performed at B97-D3 and M06-2× levels of theory. We studied the ability of mini-helixes to retain the conformation of B-DNA in the gas phase and under the influence of water bulk, uncompensated charges, and counter-ions. The def2-SV(P) and 6-31G(d,p) basis sets have been used for B97-D3 and M06-2× calculations, correspondently. To estimate basis set superposition error, the recently developed semi-empirical procedure that calls geometrical counterpoise type correction for inter- and intra-molecular basis set superposition error (gcp) has been used in the case of def2-SV(P) basis set. We found that both considered DFT functionals predict very similar results for geometrical ad energetic characteristics. We also found that in contrast to average classical molecular dynamics and data of simple geometrical models, both considered DFT functionals predict the existence of duplex specific geometries. A prediction of interaction energies of d(A)3d(T)3 and d(G)3d(C)3 duplexes accomplished in this study also verifies the applied models and confirms reliability of the new computational gcp technique.
- Published
- 2017
33. Low-melting molecular complexes. Part 5. Co-crystals of tetrahydrofuran and diethyl ether with methyl halides
- Author
-
Judith A. K. Howard, Roman I. Zubatyuk, Dmitry S. Yufit, and Oleg V. Shishkin
- Subjects
Inorganic Chemistry ,chemistry.chemical_compound ,chemistry ,In situ crystallization ,Organic chemistry ,Halide ,General Materials Science ,Diethyl ether ,Condensed Matter Physics ,Tetrahydrofuran - Abstract
The molecular complexes of tetrahydrofuran (THF) and diethyl ether (DEE) with chloroform (CF), dichlodromethane (DCM) and bromoform (BF) have been synthesised by in situ cryo-crystallization and their structures have been determined by single-crystal X-ray diffraction. CF forms 2:1 co-crystals with THF and DEE, where the components are linked in isolated 2:1 complexes by Cl3 C-H…O interactions. Molecules of components in THF-BF complex form halogen-bonded chains, while the complexes DCM and BF with DEE contain two independent pairs of the components linked by C-H…O contacts. Supramolecular architecture of the molecular complexes is analysed using energy-based topology of intermolecular interactions.
- Published
- 2014
34. Trimethyltrioxane (Paraldehyde) and Its Halomethanes Complexes: Crystallization, Structures, and Analysis of Packing Motifs
- Author
-
Roman I. Zubatyuk, Dmitry S. Yufit, Oleg V. Shishkin, and Judith A. K. Howard
- Subjects
Chloroform ,Stereochemistry ,Intermolecular force ,General Chemistry ,Condensed Matter Physics ,Dibromomethane ,law.invention ,chemistry.chemical_compound ,Crystallography ,chemistry ,law ,General Materials Science ,Isostructural ,Crystallization ,Bromoform ,Single crystal ,Dichloromethane - Abstract
Crystals of molecular complexes of trimethyltrioxane (TMT) with chloroform (CF), bromoform (BF), dichloromethane (DCM), and dibromomethane (DBM) as well as those of pure TMT were grown in situ and characterized by single crystal X-ray crystallography. The CF and BF complexes, as well as those of DCM and DBM, are isostructural. The packing motifs were examined using the vector analysis of pairwise energies of intermolecular interactions. The method shows some deficiencies of the traditional approach based on the analysis of geometrical parameters of short intermolecular contacts.
- Published
- 2014
35. Synthesis of 1R-1H-Imidazo[1,2-a]pyridin-4-ium-8-olate Derivatives
- Author
-
Volodymyr O. Kovtunenko, L. M. Potikha, Oleg V. Shishkin, Andriy V. Shelepyuk, and Roman I. Zubatyuk
- Subjects
Chemistry ,Elemental analysis ,Organic Chemistry ,Carbon-13 NMR ,Combinatorial chemistry - Abstract
A new method based on reaction of 4-bromobut-2-enoates with N-alkylimidazoles was proposed for obtaining 1R-1H-imidazo[1,2-a]pyridin-4-ium-8-olate and 1-R-8-methoxy-1H-imidazo[1,2-a]pyridin-4-ium derivatives. The structures of synthesized compounds were confirmed by 1H, 13C NMR, elemental analysis, and X-ray data.
- Published
- 2014
36. Role of CHF2- and CF3-Substituents on Molecular Arrangement in the Solid State: Experimental and Theoretical Crystal Structure Analysis of CH3/CHF2/CF3-Substituted Benzene
- Author
-
Roman I. Zubatyuk, Klaus Merz, Felix Uhl, Mathies V. Evers, and Oleg V. Shishkin
- Subjects
Diffraction ,Trifluoromethyl ,Materials science ,Ab initio ,Solid-state ,General Chemistry ,Crystal structure ,Condensed Matter Physics ,Crystal ,chemistry.chemical_compound ,Crystallography ,chemistry ,General Materials Science ,Benzene ,Diffractometer - Abstract
The influence of CH3/CHF2/CF3-exchange on the molecular arrangement in the solid state of the low melting compounds α-toluene 1, (difluoromethyl)benzene 2, and (trifluoromethyl)benzene 3 was investigated by crystal structure determinations and theoretical calculations. The compounds were crystallized by in situ crystallization directly on the diffractometer and analyzed by X-ray diffraction. The crystal packing motifs were also analyzed based on ab initio quantum-chemical calculations of the intermolecular interaction energy, using the B97-D3/def2-TZVP method.
- Published
- 2014
37. A Theoretical Investigation of the Relative Stability of Isomeric Dihydropyridines
- Author
-
Oleg V. Shishkin, Sergey M. Desenko, Roman I. Zubatyuk, and Jerzy Leszczynski
- Subjects
chemistry.chemical_compound ,chemistry ,Atomic orbital ,Computational chemistry ,Organic Chemistry ,Molecule ,Density functional theory ,Methylene ,Conjugated system ,Hyperconjugation ,Ring (chemistry) ,Antiaromaticity - Abstract
The molecular structure and relative stability of isomeric dihydropyridines have been calculated using the density functional theory and the Moller–Plesset second-order perturbation theory. The results of the calculations demonstrate that 3,4- and 2,3-dihydropyridines are the most stable species despite the presence of a 4π-electron conjugated system within the ring. A comparison of the relative energy of acyclic analogs of dihydropyridines indicates that this is caused by the internal properties of the conjugated system. The remaining dihydropyridines are strongly destabilized by the formation of antiaromatic conjugated (or quasi-conjugated) systems due to the interaction of pz atomic orbitals of the carbon and nitrogen atoms with the pseudo-π fragment orbital of the methylene group. Application of the more accurate CCSD(T)/CBS method results in considerable stabilization of 1,4-dihydropyridine. However, the order of stability of other isomers remains the same as it was found at the MP2 level of theory.
- Published
- 2014
38. A Theoretical Structural Study of Isoniazid Complexes with Thiotriazoline
- Author
-
I. A. Mazur, O. V. Khromyleva, Roman I. Zubatyuk, Oleg V. Shishkin, and L. I. Kucherenko
- Subjects
Aqueous solution ,Stereochemistry ,Organic Chemistry ,Isoniazid ,Antituberculosis agent ,Quantum chemistry ,Gas phase ,chemistry.chemical_compound ,chemistry ,Computational chemistry ,Morpholine ,medicine ,Molecule ,Solvent effects ,medicine.drug - Abstract
A combined molecular mechanics and quantum chemistry modeling was performed for investigation of the structure and relavive stability of two- and three-component complexes formed by the antituberculosis agent isoniazid with morpholinium (3-methyl-1,2,4-triazol-5-yl)thioacetate (MTTA). The possible interactions between the molecules were identified by molecular mechanics calculations, and the stability of the complexes was calculated by the density functional method B97-D/6-311G**, with accounting for the solvent effects in the SMD continuum model. The calculations showed that stable complexes of isoniazid with this thiatriazoline are possible both in the gas phase (ΔG298 = -13.6 kcal/mol) and in aqueous solution (ΔG298 = -7.6 kcal/mol). The formation of two-component complexes between isoniazid and MTTA without involving morpholine is considerably less favored (ΔG298 = -6.6 kcal/mol in the gas phase and ΔG298 = -2.6 kcal/mol in solution). Thus, morpholine may be considered as a component facilitating the formation of isoniazid complexes with MTTA.
- Published
- 2014
39. Investigation of topology of intermolecular interactions in the benzene–acetylene co-crystal by different theoretical methods
- Author
-
Oleg V. Shishkin, Roman I. Zubatyuk, Roland Boese, and Andrey V. Maleev
- Subjects
Crystal ,Coordination sphere ,Chemistry ,Intermolecular force ,Molecule ,Quantum-mechanical explanation of intermolecular interactions ,Interaction energy ,Crystal structure ,Physics::Chemical Physics ,Physical and Theoretical Chemistry ,Condensed Matter Physics ,Topology ,Topology (chemistry) - Abstract
Crystal structure of benzene–acetylene co-crystal was analysed based on calculated energies of intermolecular interactions between basic molecules located in asymmetric part of unit cell and their neighbours belonging to their first coordination sphere. It is demonstrated that the basic structural motif of the crystal is represented by infinite chains formed by the hydrogen-bonded benzene and acetylene molecules. Energy of interaction of the basic pair of molecules to neighbours within the chain is 2.2 times higher than the energy of interactions with molecules of any neighbouring chain. This ratio almost does not depend on method of calculation of interaction energy. Also, results of calculations were compared with analysis of topology of electron density distribution in crystal. The possibility to find the basic structural motif of the crystal based on properties of intermolecular bond critical points is demonstrated.
- Published
- 2014
40. Synthesis of [1,2,4]triazolo[4,3-a]pyrimidin-5(1H)-ones by the Condensation of 3-Alkylamino-5-amino-1-phenyl[1,2,4]triazoles with β-Keto Esters or Diethyl Ethoxymethylenemalonate
- Author
-
Victor M. Chernyshev, Roman I. Zubatyuk, R. S. Abagyan, and A. V. Astakhov
- Subjects
Diethyl ethoxymethylenemalonate ,Acetic acid ,chemistry.chemical_compound ,Chemistry ,Organic Chemistry ,Condensation ,Medicinal chemistry - Abstract
The condensation of 3-alkylamino-5-amino-1-phenyl[1,2,4]triazoles with β-keto esters or diethyl ethoxymethylenemalonate in the presence of acetic acid proceeds selectively to give 3-alkylamino-1-phenyl[1,2,4]triazolo[4,3-a]pyrimidin-5(1H)-ones. The observed reaction pathway is explained using quantum-chemical calculations of the energies of possible isomeric heterocyclization products.
- Published
- 2014
41. Synthesis and Formylation of Substituted 2-Spiropyrimidin-4-ones and Related Compounds
- Author
-
E. V. Velikaya, Oleg K. Farat, Svetlana A. Varenichenko, Roman I. Zubatyuk, Oleg V. Shishkin, and Victor I. Markov
- Subjects
chemistry.chemical_classification ,chemistry.chemical_compound ,chemistry ,Organic Chemistry ,Electrophile ,Organic chemistry ,Oxazines ,Ammonium acetate ,Toluene ,Formylation - Abstract
Treatment of cyclohexanone-2-carboxamide with cyclic ketones provides oxazine derivatives while refluxing in toluene with ammonium acetate and cyclic ketones yields substituted 2-spiropyrimidin-4-ones. Depending on the ratio of reactants, the oxazines and substituted 2-spiropyrimidin-4-ones under Vilsmeier-Haack conditions undergo formylation or an electrophilic rearrangement.
- Published
- 2013
42. N-Alkoxy-N-chloroureas in the synthesis of 3,4-dihydro-1H-2,1-benzoxazine-1-carboxamide and 1-alkoxy-1,3-dihydrobenzimidazol-2-ones
- Author
-
Remir G. Kostyanovsky, A. V. Mazepa, Vasiliy G. Shtamburg, Roman I. Zubatyuk, V. V. Shtamburg, and Oleg V. Shishkin
- Subjects
chemistry.chemical_compound ,chemistry ,Stereochemistry ,medicine.drug_class ,Organic Chemistry ,Alkoxy group ,Urea ,medicine ,Carboxamide ,Medicinal chemistry ,Sodium acetate - Abstract
The cyclization of N-chloro-N-(2-phenylethoxy)urea in the presence of silver trifluoroacetate leads to the formation of 3,4-dihydro-1H-2,1-benzoxazine-1-carboxamide, while N-alkoxy-N'-aryl-N-chloro-ureas in the presence of sodium acetate form 1-alkoxy-1,3-dihydrobenzimidazol-2-ones. The structures of 3,4-dihydro-1H-2,1-benzoxazine-1-carboxamide and 1-methoxy-6-nitro-1,3-dihydrobenzimidazol-2-one were examined by X-ray structural analysis.
- Published
- 2013
43. Molecular clips based on diphenylglycoluril and benzocrown ethers: promising complexing agents for the alkali metal cations
- Author
-
Roman I. Zubatyuk, Oleg V. Shishkin, Alexander Yu. Lyapunov, Tatiana Yu. Bogaschenko, Tatiana I. Kirichenko, Catherine Yu. Kulygina, and Leonid S. Kikot
- Subjects
chemistry.chemical_classification ,Cation binding ,Picrate ,education ,Inorganic chemistry ,General Chemistry ,Condensed Matter Physics ,Alkali metal ,chemistry.chemical_compound ,chemistry ,Polymer chemistry ,Moiety ,Molecule ,Selectivity ,Molecular tweezers ,Crown ether ,Food Science - Abstract
The interaction of new molecular clips containing diphenylglycoluril and benzocrown ethers moieties with alkali metals ions was studied. Stability constants were determined by spectrophotometric titrations with chloride salts in methanol. Complex stability and cation binding selectivity were shown to be dependent on the size of the crown ether moiety. The “sandwich-type” 1:1 (clip to cation) complexes and the “classical” 1:2 complexes were found. Their ratio varies depending on the molecular clips nature and on the cation type. It was found an unexpected selectivity of the molecular clip with benzo-15-crown-5 moieties toward K+ and Rb+ cations. The molecular structure of the clip complex with benzo-15-crown-5 fragments and sodium picrate was determined by X-ray crystallography. The crystal structure and solution-state structure were proven to be similar.
- Published
- 2013
44. Anion···π-system interactions in crystals of 4-amino-1-(β-phenylethyl)-1,2,4-triazolium bromide
- Author
-
G. V. Georgievskii, L. I. Kucherenko, Roman I. Zubatyuk, I. A. Mazur, Oleg V. Shishkin, N. V. Parnyuk, and Svitlana V. Shishkina
- Subjects
Diffraction ,Crystal ,Quantum chemical ,chemistry.chemical_compound ,Crystallography ,Character (mathematics) ,chemistry ,Bromide ,Inorganic chemistry ,Intermolecular force ,General Chemistry ,Ion - Abstract
The character of intermolecular interactions of the bromide anion and organic cation in crystal of 4-amino-1-(β-phenylethyl)-1,2,4-triazolium bromide was studied by a combination of X-ray diffraction data and M06-2X/cc-pvtz quantum chemical calculations. The existence of binding anion...π-system interactions was shown, and their characteristics were studied.
- Published
- 2013
45. Bifunctionalization of a mixture of 2-chloro-and 2-bromo-N-ethoxycarbonylmethylpyridinium halides by arylmethylidenemalononitriles in basic medium
- Author
-
Roman I. Zubatyuk, N. M. Tverdokhleb, Oleg V. Shishkin, and G. E. Khoroshilov
- Subjects
chemistry.chemical_compound ,Chemistry ,Aryl ,Organic Chemistry ,Condensation ,Halide ,Organic chemistry ,Nuclear magnetic resonance spectroscopy ,Medicinal chemistry - Abstract
The two-component condensation of 2-chloro- or 2-bromo-N-ethoxycarbonylmethylpyridinium halides and aryl- or hetarylmethylidenemalononitriles gave ethyl 2-[2-(dicyanomethylidene)pyridin-1(2H)-yl]-3-arylacrylates. Correlation NMR spectroscopy and X-ray diffraction structural analysis allowed the structural characterization of these products.
- Published
- 2013
46. Synthesis and aminomethylation of 9-aza-3-azoniaspiro[5,5]undeca-7,10-diene-8-selenolates
- Author
-
Sergey G. Krivokolysko, V. V. Dotsenko, K. A. Frolov, Oleg V. Shishkin, and Roman I. Zubatyuk
- Subjects
chemistry.chemical_compound ,Diene ,Chemistry ,Stereochemistry ,Organic Chemistry ,Mannich reaction ,Ene reaction ,Malononitrile - Abstract
10-Amino-7,11-dicyano-9-aza-3-azoniaspiro[5,5]undeca-7,10-diene-8-selenolates have been obtained by the interaction of N-alkylpiperidin-4-ones with 2 equiv. cyanoselenoacetamide or with malononitrile and cyanoselenoacetamide. Aminomethylation of the obtained compounds proceeded under mild conditions and led to the formation of 8'-selenoxo-3',5',7',11'-tetraazaspiro[piperidine-4,13'-tri-cyclo[7.3.1.02,7]tridec[2]ene]-1',9'-dicarbonitriles. The structure of 1-methyl-5',11'-di(4-methyl-phenyl)-8'-selenoxo-3',5',7',11'-tetraazaspiro[piperidine-4,13'-tricyclo[7.3.1.02,7]tridec[2]ene]-1',9'-di-carbonitrile was determined by X-ray structural analysis.
- Published
- 2013
47. Reactions of 2-(2-hetaryl)-2-(tetrahydrofuran-2-ylidene)acetonitriles with tertiary amines
- Author
-
A. V. Turov, O. V. Khilya, Oleg V. Shishkin, A. A. Chekotilo, Demyd S. Milokhov, G. V. Palamarchuk, Roman I. Zubatyuk, and Yu. M. Volovenko
- Subjects
chemistry.chemical_compound ,Acetonitriles ,chemistry ,Organic Chemistry ,Pyridine ,Medicinal chemistry ,Tetrahydrofuran - Abstract
The reactions of 2-(2-hetaryl)-2-(tetrahydrofuran-2-ylidene)acetonitriles with conformationally rigid and heterocyclic tertiary amines were investigated. Compounds with bipolar structures were obtained: 1-cyano-1-(2-hetaryl)-5-(pyridinium-1-yl)-1-penten-2-olates and 5-(4-aza-1-azoniobicyclo[2.2.2]oct-1-yl)-1-cyano-1-(2-hetaryl)pent-1-en-2-olates.
- Published
- 2013
48. Synthesis of 2-(2-hetaryl)-6-hydroxy-3-(R-amino)-2-hexenenitriles
- Author
-
Roman I. Zubatyuk, Yu. M. Volovenko, O. V. Khilya, A. V. Turov, T. A. Volovnenko, and Oleg V. Shishkin
- Subjects
Primary (chemistry) ,Acetonitriles ,Chemistry ,Stereochemistry ,Organic Chemistry ,Amination - Abstract
The reaction of 2-hetaryl-2-(tetrahydrofuran-2-ylidene)acetonitriles and 6-chloro-2-(2-hetarylidene)-3-oxohexanenitriles with amines was studied. It was shown that the reaction of primary aliphatic amines with 6-chloro-2-(2-hetarylidene)-3-oxohexanenitriles takes place through a stage involving the formation of 2-hetaryl-2-(tetrahydrofuran-2-ylidene)acetonitriles followed by opening of the furanylidene fragment of the latter and the formation of 2-(2-hetaryl)-6-hydroxy-3-(R-amino)-2-hexenenitriles.
- Published
- 2013
49. Optical properties of KDP crystals doped with pyrenetetrasulfonic acid salt
- Author
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Igor M. Pritula, Roman I. Zubatyuk, A.V. Lopin, V. M. Puzikov, O. N. Bezkrovnaya, Oleg V. Shishkin, V. Ya. Gayvoronsky, and M. I. Kolybaeva
- Subjects
chemistry.chemical_classification ,Materials science ,Doping ,Inorganic chemistry ,Analytical chemistry ,Salt (chemistry) ,General Chemistry ,Condensed Matter Physics ,Excimer ,Crystal ,chemistry.chemical_compound ,chemistry ,Luminophore ,Molecule ,Acid salt ,General Materials Science ,Luminescence - Abstract
KDP crystals with incorporated molecules of the luminophore 1,3,6,8-pyrenetetrasulfonic acid tetrasodium salt (SPA) were grown from KH 2 PO 4 solutions by the temperature lowering method. The luminescence spectra of KDP/SPA crystals and SPA solutions in distilled water and in KH 2 PO 4 solutions, were studied. The increase of the dye content gives rise to excimer luminescence in the solutions and in KDP crystals, which is due to the formation of associated dye molecules. SPA molecules possessing negative electrostatic potential are incorporated into the pyramidal growth sector of KDP crystal.
- Published
- 2013
50. Tin(IV) complexes with 2-hydroxybenz-(2-hydroxynaphth)aldehyde picolinoylhydrazones (H2Ps, H2Pnf). Crystal structure of [SnCl3(Ps · H)] · CH3OH and [SnCl3(Pnf · H)] · CH3OH
- Author
-
N. V. Shmatkova, Roman I. Zubatyuk, A. V. Mazepa, Oleg V. Shishkin, and I. I. Seifullina
- Subjects
chemistry.chemical_classification ,Chemistry ,Ligand ,Materials Science (miscellaneous) ,chemistry.chemical_element ,Protonation ,Crystal structure ,Photochemistry ,Aldehyde ,Inorganic Chemistry ,chemistry.chemical_compound ,Crystallography ,Pyridine ,Mass spectrum ,Physical and Theoretical Chemistry ,Tin ,Imide - Abstract
The reactions of SnCl4 with picolinoylhydrazones of 2-hydroxybenz-(2-hydroxynaphth)aldehydes (H2Ps, H2Pnf) in CH3OH gave non-electrolyte complexes [SnCl3(Ps · H)] · CH3OH (I) and [SnCl3(Pnf · H)] · CH3OH (II). The imide form of the ligand coordinated to Sn(IV) through the azomethine nitrogen atom and oxyazine and oxy oxygen atoms was proved by UV/Vis, IR, and 1H NMR spectroscopy. The negative charge on the coordination unit thus arising is counterbalanced by the positive charge caused by the protonation of ligands at the pyridine nitrogen atom of the heterocycle. It was shown that dehydrochlorination of the complexes affords tin-containing species, which correlates with the presence of the corresponding peaks [SnCl2(Ps)]+ and [SnCl2(Pnf)]+ in their mass spectra. The molecular and crystal structures of complexes I and II were determined by X-ray diffraction.
- Published
- 2013
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