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Dos Santos KA, Chaves LL, Nadvorny D, de La Roca Soares MF, Sobrinho JLS. Exploring Co-Amorphous Formulations Of Nevirapine: Insights From Computational, Thermal, And Solubility Analyses. AAPS PharmSciTech 2024; 25:214. [PMID: 39266781 DOI: 10.1208/s12249-024-02932-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 09/03/2024] [Indexed: 09/14/2024] Open
Abstract
This study aimed to assess the formation of nevirapine (NVP) co-amorphs systems (CAM) with different co-formers (lamivudine-3TC, citric acid-CAc, and urea) through combined screening techniques as computational and thermal studies, solubility studies; in addition to develop and characterize suitable NVP-CAM. NVP-CAM were obtained using the quench-cooling method, and characterized by differential scanning calorimetry (DSC), X-ray diffractometry (XRD), Fourier Transform Infrared Spectroscopy (FTIR), and polarized light microscopy (PLM), in addition to in vitro dissolution in pH 6.8. The screening results indicated intermolecular interactions occurring between NVP and 3TC; NVP and CAc, where shifts in the melting temperature of NVP were verified. The presence of CAc impacted the NVP equilibrium solubility, due to hydrogen bonds. DSC thermograms evidenced the reduction and shifting of the endothermic peaks of NVP in the presence of its co-formers, suggesting partial miscibility of the compounds. Amorphization was proven by XRD and PLM assays. In vitro dissolution study exhibited a significant increase in solubility and dissolution efficiency of NVP-CAM compared to free NVP. Combined use of screening studies was useful for the development of stable and amorphous NVP-CAM, with increased NVP solubility, making CAM promising systems for combined antiretroviral therapy.
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Affiliation(s)
- Kayque Almeida Dos Santos
- Quality Control Core of Medicines and Correlates - NCQMC, Department of Pharmaceutical Sciences, Federal University of Pernambuco, Recife, PE, Brazil
| | - Luíse Lopes Chaves
- Quality Control Core of Medicines and Correlates - NCQMC, Department of Pharmaceutical Sciences, Federal University of Pernambuco, Recife, PE, Brazil
- Postgraduate Program in Pharmaceutical Sciences, Pharmaceutical Sciences Institute, Federal University of Alagoas, Maceió, Alagoas, Brazil
| | - Daniela Nadvorny
- Postgraduate Program in Pharmaceutical Sciences, Pharmaceutical Sciences Institute, Federal University of Alagoas, Maceió, Alagoas, Brazil
| | - Mônica Felts de La Roca Soares
- Quality Control Core of Medicines and Correlates - NCQMC, Department of Pharmaceutical Sciences, Federal University of Pernambuco, Recife, PE, Brazil
- Postgraduate Program in Pharmaceutical Sciences, Pharmaceutical Sciences Institute, Federal University of Alagoas, Maceió, Alagoas, Brazil
| | - José Lamartine Soares Sobrinho
- Quality Control Core of Medicines and Correlates - NCQMC, Department of Pharmaceutical Sciences, Federal University of Pernambuco, Recife, PE, Brazil.
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2
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Rettig A, Lee J, Head-Gordon M. Even Faster Exact Exchange for Solids via Tensor Hypercontraction. J Chem Theory Comput 2023; 19:5773-5784. [PMID: 37586065 DOI: 10.1021/acs.jctc.3c00407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Hybrid density functional theory (DFT) remains intractable for large periodic systems due to the demanding computational cost of exact exchange. We apply the tensor hypercontraction (THC) (or interpolative separable density fitting) approximation to periodic hybrid DFT calculations with Gaussian-type orbitals using the Gaussian plane wave approach. This is done to lower the computational scaling with respect to the number of basis functions (N) and k-points (Nk) at a fixed system size. Additionally, we propose an algorithm to fit only occupied orbital products via THC (i.e., a set of points, NISDF) to further reduce computation time and memory usage. This algorithm has linear scaling cost with k-points, no explicit dependence of NISDF on basis set size, and overall cubic scaling with unit cell size. Significant speedups and reduced memory usage may be obtained for moderately sized k-point meshes, with additional gains for large k-point meshes. Adequate accuracy can be obtained using THC-oo-K for self-consistent calculations. We perform illustrative hybrid density function theory calculations on the benzene crystal in the basis set and thermodynamic limits to highlight the utility of this algorithm.
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Affiliation(s)
- Adam Rettig
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Joonho Lee
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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3
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Singh MK. Controlling the aqueous growth of urea crystals with different growth inhibitors: a molecular-scale study. RSC Adv 2021; 11:12938-12950. [PMID: 35423801 PMCID: PMC8697337 DOI: 10.1039/d0ra10401a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/17/2021] [Indexed: 11/21/2022] Open
Abstract
Molecular scale understanding of the mechanism of solution-mediated nucleation and the growth of crystalline materials in the presence of growth inhibitors together with the process parameters continues to attract the interest of the scientific community though much headway has been made in recent years. Growth inhibitors can be added to solution of a crystallizing parent molecule to alter the rate of growth of different crystal faces, size and shape of the crystalline materials. In this work, we investigated the effects of a number of shape-controlling inhibitors, such as acetone, biuret and biurea, on the growth kinetics of the various faces of aqueous-grown urea crystals as a means to predictably control the crystal growth morphology. We combined the adsorption energy landscape of various auxiliaries with the kinetics of the molecular growth processes to develop an analytical model to compute the rate of growth as a function of supersaturation and the additive concentration. The model relates the kinetic and thermodynamic aspects of the adsorption of the solute, solvent and additive to provide a quantitative description of the crystal growth. Ab initio periodic dispersion-corrected density functional theory using the hybrid exchange-correlation functional was employed to determine the interfacial structure of the adsorption of various auxiliaries at crystalline surfaces. The calculated adsorption energies of different auxiliaries were employed to examine the role played by these auxiliaries during the aqueous crystallization of urea crystals containing small amounts of additives. Our results showed that the growth of (110), (111) and (1̄1̄1̄) faces were nearly unaltered by the addition of moderate amounts of acetone as it has lower adsorption energies with the surfaces of these faces. Nevertheless, the presence of acetone in the solution reasonably impeded the growth of the (001) face. The addition of biuret or biurea in the solution led to a higher adsorption energy at (001) and (111) faces. Consequently, the low concentration of these additives severely obstructed the growth of (001) and (111) faces as most of the adsorption sites were occupied by these additives. On the other hand, these additives were weakly adsorbed at the (110) face and, hence, the growth of the (110) face largely remained unaltered. Moreover, unlike biuret, biurea considerably inhibited the growth of the (1̄1̄1̄) face. Our results are in agreement with the experimental and computational results reported in the literature.
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Affiliation(s)
- M K Singh
- Theory & Simulation Laboratory, Human Resource Development Section, Raja Ramanna Centre for Advanced Technology Indore India +91-731-248-8677
- Homi Bhabha National Institute, Raja Ramanna Centre for Advanced Technology, Department of Atomic Energy Indore India
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4
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Graf W, Pearson J, Appadoo D, Robertson E, Ennis C. The prediction of far-infrared spectra for molecular crystals of forensic interest – Phenylethylamine, ephedrine & pseudoephedrine. Forensic Chem 2020. [DOI: 10.1016/j.forc.2019.100204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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5
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Brand HEA, Gu Q, Kimpton JA, Auchettl R, Ennis C. Crystal structure of propionitrile (CH 3CH 2CN) determined using synchrotron powder X-ray diffraction. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:212-216. [PMID: 31868754 DOI: 10.1107/s1600577519015911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 11/25/2019] [Indexed: 06/10/2023]
Abstract
The structure and thermal expansion of the astronomical molecule propionitrile have been determined from 100 to 150 K using synchrotron powder X-ray diffraction. This temperature range correlates with the conditions of Titan's lower stratosphere, and near surface, where propionitrile is thought to accumulate and condense into pure and mixed-nitrile phases. Propionitrile was determined to crystallize in space group, Pnma (No. 62), with unit cell a = 7.56183 (16) Å, b = 6.59134 (14) Å, c = 7.23629 (14), volume = 360.675 (13) Å3 at 100 K. The thermal expansion was found to be highly anisotropic with an eightfold increase in expansion between the c and b axes. These data will prove crucial in the computational modelling of propionitrile-ice systems in outer Solar System environments, allowing us to simulate and assign vibrational peaks in the infrared spectra for future use in planetary astronomy.
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Affiliation(s)
- Helen E A Brand
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Qinfen Gu
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Justin A Kimpton
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Rebecca Auchettl
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Courtney Ennis
- University of Otago, PO Box 56, Dunedin 9054, New Zealand
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6
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Červinka C, Fulem M. Cohesive properties of the crystalline phases of twenty proteinogenic α-aminoacids from first-principles calculations. Phys Chem Chem Phys 2019; 21:18501-18515. [PMID: 31411212 DOI: 10.1039/c9cp03102b] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cohesive properties (lattice and cohesive energy of the crystal and corresponding sublimation enthalpy) of the complete set of twenty enantiopure anhydrous proteinogenic amino acids are investigated using first-principles calculations. In contrast to neutral amino acid molecules in the vapor phase, all amino acids form crystals in their zwitterionic form. Therefore, reliable ab initio calculations of the proton transfer energy are an indispensable step of such calculations. Simplifying procedures, designed to rationalize the computational cost of the quasi-harmonic approximation, which proves too demanding if performed fully at the given quantum level of theory, are presented and tested. For this purpose, atomic multipoles (up to the quadrupoles) for the amoeba force field are parametrized for all amino acid zwitterions. While the calculated lattice energies of the amino acids range from 235-458 kJ mol-1 in absolute value, the proton transfer energies typically amount to 100-220 kJ mol-1, which translates to sublimation enthalpies ranging from 117-202 kJ mol-1, appreciably exceeding the sublimation enthalpy values common for nonionic molecular crystals. Critically assessed experimental data on sublimation enthalpies are used as a benchmark for comparison of the data calculated in this work. Cohesive properties of most amino acids calculated in this work, combining the PBE-D3(BJ)/PAW and CCSD(T)-F12/aug-cc-pVDZ levels of theory used for predictions of the lattice energies and of the proton transfer energies, respectively, exhibit a reasonable agreement with the experiment. At the same time, this work contains the first published data on cohesive properties for several enantiopure amino acids.
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Affiliation(s)
- Ctirad Červinka
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic.
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7
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Zagorac D, Müller H, Ruehl S, Zagorac J, Rehme S. Recent developments in the Inorganic Crystal Structure Database: theoretical crystal structure data and related features. J Appl Crystallogr 2019; 52:918-925. [PMID: 31636516 PMCID: PMC6782081 DOI: 10.1107/s160057671900997x] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/12/2019] [Indexed: 11/12/2022] Open
Abstract
The Inorganic Crystal Structure Database (ICSD) is the world's largest database of fully evaluated and published crystal structure data, mostly obtained from experimental results. However, the purely experimental approach is no longer the only route to discover new compounds and structures. In the past few decades, numerous computational methods for simulating and predicting structures of inorganic solids have emerged, creating large numbers of theoretical crystal data. In order to take account of these new developments the scope of the ICSD was extended in 2017 to include theoretical structures which are published in peer-reviewed journals. Each theoretical structure has been carefully evaluated, and the resulting CIF has been extended and standardized. Furthermore, a first classification of theoretical data in the ICSD is presented, including additional categories used for comparison of experimental and theoretical information.
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Affiliation(s)
- D Zagorac
- Technicum Scientific Publishing, Stuttgart, Germany
- Institute of Nuclear Sciences Vinča, Materials Science Laboratory, Belgrade University, Belgrade, Serbia
| | - H Müller
- FIZ Karlsruhe - Leibniz Institute for Information Infrastructure, Karlsruhe, Germany
| | - S Ruehl
- FIZ Karlsruhe - Leibniz Institute for Information Infrastructure, Karlsruhe, Germany
| | - J Zagorac
- Technicum Scientific Publishing, Stuttgart, Germany
- Institute of Nuclear Sciences Vinča, Materials Science Laboratory, Belgrade University, Belgrade, Serbia
| | - S Rehme
- FIZ Karlsruhe - Leibniz Institute for Information Infrastructure, Karlsruhe, Germany
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8
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Xavier NF, Da Silva AM, Bauerfeldt GF. Supercell calculations of the geometry and lattice energy of α-glycine crystal. J Mol Model 2019; 25:244. [PMID: 31342179 DOI: 10.1007/s00894-019-4124-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 07/07/2019] [Indexed: 01/01/2023]
Abstract
Evidence about the presence of glycine in the interstellar medium (ISM) has been motivating studies aiming the understanding of the chemical behavior of this amino acid in such environment. Since glycine is expected to be predominantly found in the ISM in solid phase, this work focuses on the search for a theoretical methodology for obtaining a molecular cluster for α-glycine that provides a good description of the geometry of the unit cell and lattice energy. Calculations have been performed using the B3LYP-D3, PBE0-D3, and WB97X-D3 functionals, with def2-SVP, def2-TZVP, def2-TZVPP, and def2-QZVPP basis sets for two models: (a) the unit cell, containing 4 glycine units, and (b) the 2 × 1 × 2 expanded cell, with 16 glycine units. Corrections for the basis set superposition error have also been applied. No significant changes in geometries and lattice energy predictions from the different functionals and basis sets have been observed for each model. Nevertheless, results obtained for the larger molecular cluster are in better agreement with the experimental data. The best lattice energy prediction, obtained for the 2 × 1 × 2 supercell at the B3LYP-gCP-D3/def2-TZVPP level, is - 15.35 kcal mol-1, with a root mean square deviation of the predicted Cartesian coordinates of the inner molecules (with respect to the experimental α-glycine unit cell geometry) of 0.966 Å. This methodology is finally recommended for future studies of similar molecular cluster, and the predicted geometry is proposed for further studies aiming to describe glycine surface reactions in the ISM.
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Affiliation(s)
- Neubi F Xavier
- Instituto de Química, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, 23890-000, Brazil
| | - Antônio M Da Silva
- Instituto de Química, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, 23890-000, Brazil
| | - Glauco Favilla Bauerfeldt
- Instituto de Química, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, 23890-000, Brazil.
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9
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Butera V, Fukaya N, Choi J, Sato K, Choe Y. Mechanistic Details on the Conversion of Si–O to Si–C Bonds Using Metal Hydrides: A Density Functional Theory Study. Eur J Inorg Chem 2019. [DOI: 10.1002/ejic.201900039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Valeria Butera
- Research Center for Computational Design of Advanced Functional Materials (CD‐FMat) National Institute of Advanced Industrial Science and Technology (AIST) 1‐1–1 Umezono 305‐8568 Tsukuba Japan
| | - Norihisa Fukaya
- Interdisciplinary Research Center for Catalytic Chemistry National Institute of Advanced Industrial Science and Technology (AIST) 1‐1–1 Higashi Tsukuba 305‐8568 Japan
| | - Jun‐Chul Choi
- Interdisciplinary Research Center for Catalytic Chemistry National Institute of Advanced Industrial Science and Technology (AIST) 1‐1–1 Higashi Tsukuba 305‐8568 Japan
| | - Kazuhiko Sato
- Interdisciplinary Research Center for Catalytic Chemistry National Institute of Advanced Industrial Science and Technology (AIST) 1‐1–1 Higashi Tsukuba 305‐8568 Japan
| | - Yoong‐Kee Choe
- Research Center for Computational Design of Advanced Functional Materials (CD‐FMat) National Institute of Advanced Industrial Science and Technology (AIST) 1‐1–1 Umezono 305‐8568 Tsukuba Japan
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10
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Gladfelter WL, Cramer CJ. Impact of dihydrogen bonding on lattice energies and sublimation enthalpies of crystalline [H 2GaNH 2] 3, [H 2BNH 2] 3 and [H 2GeCH 2] 3. RSC Adv 2019; 9:29448-29455. [PMID: 35528427 PMCID: PMC9071838 DOI: 10.1039/c9ra07144j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 09/11/2019] [Indexed: 11/21/2022] Open
Abstract
Calculated lattice energies and sublimation enthalpies provide quantitative measures of the importance of intermolecular dihydrogen bonds.
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Affiliation(s)
| | - Christopher J. Cramer
- Department of Chemistry
- Chemical Theory Center
- Minnesota Supercomputing Institute
- University of Minnesota
- Minneapolis
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11
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Červinka C, Beran GJO. Towards reliable ab initio sublimation pressures for organic molecular crystals - are we there yet? Phys Chem Chem Phys 2019; 21:14799-14810. [PMID: 31225538 DOI: 10.1039/c9cp01572h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Knowledge of molecular crystal sublimation equilibrium data is vital in many industrial processes, but this data can be difficult to measure experimentally for low-volatility species. Theoretical prediction of sublimation pressures could provide a useful supplement to experiment, but the exponential temperature dependence of sublimation (or any saturated vapor) pressure curve makes this challenging. An uncertainty of only a few percent in the sublimation enthalpy or entropy can propagate to an error in the sublimation pressure exceeding several orders of magnitude for a given temperature interval. Despite this fundamental difficulty, this paper performs some of the first ab initio predictions of sublimation pressure curves. Four simple molecular crystals (ethane, methanol, benzene, and imidazole) have been selected for a case study showing the currently achievable accuracy of quantum chemistry calculations. Fragment-based ab initio techniques and the quasi-harmonic approximation are used for calculations of cohesive and phonon properties of the crystals, while the vapor phase is treated by the ideal gas model. Ab initio sublimation pressure curves for model compounds are compared against their experimental counterparts. The computational uncertainties are estimated, weak points of the computational methodology are identified, and further improvements are proposed.
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Affiliation(s)
- Ctirad Červinka
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic.
| | - Gregory J O Beran
- Department of Chemistry, University of California, Riverside, California 92521, USA
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12
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Gionda A, Macetti G, Loconte L, Rizzato S, Orlando AM, Gatti C, Lo Presti L. A variable-temperature X-ray diffraction and theoretical study of conformational polymorphism in a complex organic molecule (DTC). RSC Adv 2018; 8:38445-38454. [PMID: 35559076 PMCID: PMC9090575 DOI: 10.1039/c8ra08063a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/07/2018] [Indexed: 11/28/2022] Open
Abstract
Two conformational crystal polymorphs of 3-diethylamino-4-(4-methoxyphenyl)-1,1-dioxo-4H-1λ6,2-thiazete-4-carbonitrile (DTC) have been analyzed in the 100 K-room temperature range by single crystal X-ray diffraction and high quality DFT calculations. DTC has strongly polar as well as aliphatic substituents but no hydrogen bonding groups, and thus qualifies as a test molecule for the relative importance of electrostatic vs. dispersion–repulsion terms. The two polymorphs have the same P21/n space group and differ by a flipping of the –OCH3 group, the two conformations being almost equi-energetic and separated by a low barrier. The system is monotropic in the observed temperature range with nearly identical thermal expansion coefficients and energy–temperature slopes, one phase consistently predicted to be more stable in agreement with the relative ease of appearance. Energy decompositions show that the electrostatic term is dominant and stabilizes with decreasing temperature. Dispersion and repulsion show the expected behavior, the former becoming more stabilizing at lower temperature in contrast with increasing repulsion at higher density. Absolute values and trends are very similar in the two phases, explaining the small total energy difference. Geometrical analyses of intermolecular contacts using fingerprint plots, as well as the study of molecular dipole moments as a function of T in the framework of the Quantum Theory of Atoms in Molecules, reveal more details of phase stability. A small conformational change in the asymmetric unit has a significant effect on how non-covalent interactions determine (i) the crystal packing and (ii) the effect of T on the relative balance of electrostatics and dispersion–repulsions.![]()
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Affiliation(s)
- Andrea Gionda
- Università degli Studi di Milano
- Department of Chemistry
- Italy
| | - Giovanni Macetti
- Università degli Studi di Milano
- Department of Chemistry
- Italy
- Centre for Materials Crystallography
- Århus University
| | - Laura Loconte
- Università degli Studi di Milano
- Department of Chemistry
- Italy
| | - Silvia Rizzato
- Università degli Studi di Milano
- Department of Chemistry
- Italy
| | | | - Carlo Gatti
- Centre for Materials Crystallography
- Århus University
- Denmark
- Istituto di Scienze e Tecnologie Molecolari
- Italian CNR
| | - Leonardo Lo Presti
- Università degli Studi di Milano
- Department of Chemistry
- Italy
- Centre for Materials Crystallography
- Århus University
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13
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Surov AO, Voronin AP, Vener MV, Churakov AV, Perlovich GL. Specific features of supramolecular organisation and hydrogen bonding in proline cocrystals: a case study of fenamates and diclofenac. CrystEngComm 2018. [DOI: 10.1039/c8ce01458b] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
New zwitterionic cocrystals of fenamate drugs and diclofenac with the naturally occurring amino acid l-proline have been obtained and thoroughly characterised by a variety of experimental and theoretical techniques.
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Affiliation(s)
- Artem O. Surov
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences
- 153045 Ivanovo
- Russia
| | - Alexander P. Voronin
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences
- 153045 Ivanovo
- Russia
| | | | - Andrei V. Churakov
- N.S. Kurnakov Institute of General and Inorganic Chemistry of the Russian Academy of Sciences
- Moscow
- Russia
| | - German L. Perlovich
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences
- 153045 Ivanovo
- Russia
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14
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Ennis C, Auchettl R, Appadoo DRT, Robertson EG. The prediction of far-infrared spectra for planetary nitrile ices using periodic density functional theory with comparison to thin film experiments. Phys Chem Chem Phys 2018; 20:23593-23605. [DOI: 10.1039/c8cp04219e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The application of high accuracy periodic DFT calculations to replicate laboratory thin film spectra allowing the assignment of vibrational far-infrared modes in nitrile-bearing planetary ices.
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Affiliation(s)
- C. Ennis
- Department of Chemistry and Physics
- La Trobe Institute for Molecular Science
- La Trobe University
- Victoria
- Australia
| | - R. Auchettl
- Department of Chemistry and Physics
- La Trobe Institute for Molecular Science
- La Trobe University
- Victoria
- Australia
| | | | - E. G. Robertson
- Department of Chemistry and Physics
- La Trobe Institute for Molecular Science
- La Trobe University
- Victoria
- Australia
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15
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Singh MK, Banerjee A. Role of tailor-made additives in controlling vapour growth asymmetry along the polar axis of α-resorcinol crystals: a molecular-scale study. CrystEngComm 2018. [DOI: 10.1039/c8ce00118a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The role of different tailor-made additives and conformers of resorcinol have been investigated to elucidate the mechanism of unidirectional vapour growth of α-resorcinol crystal. Our results show the growth anisotropy is linked with the surface stabilization of the slow growing face.
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Affiliation(s)
- M. K. Singh
- Theory & Simulation Laboratory
- Human Resource Development Section
- Raja Ramanna Centre for Advanced Technology
- Indore
- India
| | - Arup Banerjee
- Theory & Simulation Laboratory
- Human Resource Development Section
- Raja Ramanna Centre for Advanced Technology
- Indore
- India
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16
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Červinka C, Fulem M. State-of-the-Art Calculations of Sublimation Enthalpies for Selected Molecular Crystals and Their Computational Uncertainty. J Chem Theory Comput 2017; 13:2840-2850. [PMID: 28437618 DOI: 10.1021/acs.jctc.7b00164] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A computational methodology for calculation of sublimation enthalpies of molecular crystals from first principles is developed and validated by comparison to critically evaluated literature experimental data. Temperature-dependent sublimation enthalpies for a set of selected 22 molecular crystals in their low-temperature phases are calculated. The computational methodology consists of several building blocks based on high-level electronic structure methods of quantum chemistry and statistical thermodynamics. Ab initio methods up to the coupled clusters with iterative treatment of single and double excitations and perturbative triples correction with an estimated complete basis set description [CCSD(T)/CBS] are used to calculate the cohesive energies of crystalline phases within a fragment-based additive scheme. Density functional theory (DFT) calculations with periodic boundary conditions (PBC) coupled with the quasi-harmonic approximation are used to evaluate the thermal contributions to the enthalpy of the solid phase. The properties of the vapor phase are calculated within the ideal-gas model using the rigid-rotor harmonic-oscillator model with correction for internal rotation using a one-dimensional hindered rotor approximation and a proper treatment of the molecular rotational degrees of freedom in the vicinity of 0 K. All individual terms contributing to the sublimation enthalpy as a function of temperature are discussed and their uncertainties estimated by comparison to critically evaluated experimental data.
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Affiliation(s)
- Ctirad Červinka
- Department of Physical Chemistry, University of Chemistry and Technology , Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic
| | - Michal Fulem
- Department of Physical Chemistry, University of Chemistry and Technology , Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic
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17
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Erba A, Maul J, Civalleri B. Thermal properties of molecular crystals through dispersion-corrected quasi-harmonic ab initio calculations: the case of urea. Chem Commun (Camb) 2016; 52:1820-3. [PMID: 26670006 DOI: 10.1039/c5cc08982d] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An ab initio quantum-mechanical theoretical framework is presented to compute the thermal properties of molecular crystals. The present strategy combines dispersion-corrected density-functional-theory (DFT-D), harmonic phonon dispersion, quasi-harmonic approximation to the lattice dynamics for thermal expansion and thermodynamic functions, and quasi-static approximation for anisotropic thermo-elasticity. The proposed scheme is shown to reliably describe thermal properties of the urea molecular crystal by a thorough comparison with experimental data.
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Affiliation(s)
- Alessandro Erba
- Dipartimento di Chimica, Università di Torino and Interdepartmental Centre NIS, Nanostructured Interfaces and Surfaces, Via Giuria 5, 10125 Torino, Italy.
| | - Jefferson Maul
- Dipartimento di Chimica, Università di Torino and Interdepartmental Centre NIS, Nanostructured Interfaces and Surfaces, Via Giuria 5, 10125 Torino, Italy. and Laboratório de Combustíveis e Materiais, INCTMN-UFPB, Universidade Federal da Paraíba, CEP 58051-900, João Pessoa, PB, Brazil
| | - Bartolomeo Civalleri
- Dipartimento di Chimica, Università di Torino and Interdepartmental Centre NIS, Nanostructured Interfaces and Surfaces, Via Giuria 5, 10125 Torino, Italy.
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18
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Effects of the crystal structure and thermodynamic stability on solubility of bioactive compounds: DFT study of isoniazid cocrystals. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.07.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Dierks TM, Korter TM. Origins of the Relative Stabilities of Anhydrous and Hydrated d-Mannitol Crystals. J Phys Chem A 2016; 120:6629-36. [DOI: 10.1021/acs.jpca.6b05244] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Teresa M. Dierks
- Department of Chemistry, Syracuse University, 1-014 Center for Science and Technology, Syracuse, New York 13244-4100, United States
| | - Timothy M. Korter
- Department of Chemistry, Syracuse University, 1-014 Center for Science and Technology, Syracuse, New York 13244-4100, United States
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20
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Zhang F, Wang HW, Tominaga K, Hayashi M. Mixing of intermolecular and intramolecular vibrations in optical phonon modes: terahertz spectroscopy and solid-state density functional theory. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1256] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Feng Zhang
- Molecular Photoscience Research Center; Kobe University; Kobe Japan
| | - Houng-Wei Wang
- Center for Condensed Matte Sciences; National Taiwan University; Taipei Taiwan
| | - Keisuke Tominaga
- Molecular Photoscience Research Center; Kobe University; Kobe Japan
| | - Michitoshi Hayashi
- Center for Condensed Matte Sciences; National Taiwan University; Taipei Taiwan
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21
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Rérat M, Maschio L, Kirtman B, Civalleri B, Dovesi R. Computation of Second Harmonic Generation for Crystalline Urea and KDP. An ab Initio Approach through the Coupled Perturbed Hartree–Fock/Kohn–Sham Scheme. J Chem Theory Comput 2015; 12:107-13. [DOI: 10.1021/acs.jctc.5b00791] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michel Rérat
- Equipe
de Chimie Physique, IPREM UMR5254, Université de Pau et des Pays de l’Adour, 64000 Pau, France
| | - Lorenzo Maschio
- Dipartimento
di Chimica and NIS (Nanostructured Interfaces and Surfaces) Centre, Università di Torino, via Giuria 5, I-10125 Torino, Italy
| | - Bernard Kirtman
- Department
of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Bartolomeo Civalleri
- Dipartimento
di Chimica and NIS (Nanostructured Interfaces and Surfaces) Centre, Università di Torino, via Giuria 5, I-10125 Torino, Italy
| | - Roberto Dovesi
- Dipartimento
di Chimica and NIS (Nanostructured Interfaces and Surfaces) Centre, Università di Torino, via Giuria 5, I-10125 Torino, Italy
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22
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Francuski BM, Novaković SB, Ostojić BD, Francuski DD, Bogdanović GA. Electronic features and hydrogen bonding capacity of the sulfur acceptor in thioureido-based compounds. Part 2. Further insight by theoretical charge density study. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.05.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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23
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Singh MK. Simulating growth morphology of urea crystals from vapour and aqueous solution. CrystEngComm 2015. [DOI: 10.1039/c5ce01013f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The prediction of solvent-induced urea crystal growth shape from the internal and interfacial atomic structure was investigated. A computational model was used to calculate crystal growth morphologies from vapour and aqueous solution as a function of supersaturation; predicted growth shapes agree well with experimental observations.
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Affiliation(s)
- M. K. Singh
- Laser Materials Development and Devices Division
- Raja Ramanna Centre for Advanced Technology
- Indore, India
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24
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Medvedev AG, Shishkina AV, Prikhodchenko PV, Lev O, Vener MV. The applicability of the dimeric heterosynthon concept to molecules with equivalent binding sites. A DFT study of crystalline urea–H2O2. RSC Adv 2015. [DOI: 10.1039/c5ra02498f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The limited applicability of the dimeric heterosynthon concept to a two-component urea–H2O2crystal is reported.
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Affiliation(s)
- A. G. Medvedev
- Kurnakov Institute of General and Inorganic Chemistry
- RAS
- Moscow
- Russia
- The Casali Institute of Applied Chemistry
| | | | | | - O. Lev
- The Casali Institute of Applied Chemistry
- The Institute of Chemistry
- The Hebrew University of Jerusalem
- Jerusalem
- Israel
| | - M. V. Vener
- Kurnakov Institute of General and Inorganic Chemistry
- RAS
- Moscow
- Russia
- Mendeleev University of Chemical Technology
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25
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Wilk M, Jarzembska KN, Janczak J, Hoffmann J, Videnova-Adrabinska V. Synthesis, crystal structure and computational studies of 4-nitrobenzylphosphonic acid. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.05.052] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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26
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Vener MV, Shishkina AV, Rykounov AA, Tsirelson VG. Cl···Cl interactions in molecular crystals: insights from the theoretical charge density analysis. J Phys Chem A 2013; 117:8459-67. [PMID: 23924151 DOI: 10.1021/jp405119x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The structure, IR harmonic frequencies and intensities of normal vibrations of 20 molecular crystals with the X-Cl···Cl-X contacts of different types, where X = C, Cl, and F and the Cl···Cl distance varying from ~3.0 to ~4.0 Å, are computed using the solid-state DFT method. The obtained crystalline wave functions have been further used to define and describe quantitatively the Cl···Cl interactions via the electron-density features at the Cl···Cl bond critical points. We found that the electron-density at the bond critical point is almost independent of the particular type of the contact or hybridization of the ipso carbon atom. The energy of Cl···Cl interactions, E(int), is evaluated from the linking E(int) and local electronic kinetic energy density at the Cl···Cl bond critical points. E(int) varies from 2 to 12 kJ/mol. The applicability of the geometrical criterion for the detection of the Cl···Cl interactions in crystals with two or more intermolecular Cl···Cl contacts for the unique chlorine atom is not straightforward. The detection of these interactions in such crystals may be done by the quantum-topological analysis of the periodic electron density.
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Affiliation(s)
- Mikhail V Vener
- Department of Quantum Chemistry, Mendeleev University of Chemical Technology, Miusskaya Square 9, 125047 Moscow, Russia.
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27
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Singh MK, Sharma SK, Banerjee A. Asymmetrical growth and dissolution along polar axis of α-resorcinol crystal: role of solvent and external environment. CrystEngComm 2013. [DOI: 10.1039/c3ce41155a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Singh MK, Banerjee A. Growth and dissolution mechanism at the opposite and hemihedral faces of polar crystals. CrystEngComm 2013. [DOI: 10.1039/c3ce40282g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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King MD, Korter TM. Modified Corrections for London Forces in Solid-State Density Functional Theory Calculations of Structure and Lattice Dynamics of Molecular Crystals. J Phys Chem A 2012; 116:6927-34. [DOI: 10.1021/jp303746a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Matthew D. King
- Department of Chemistry, Syracuse University, 1-014 Center for Science & Technology, Syracuse, New York 13244-4100, United States
| | - Timothy M. Korter
- Department of Chemistry, Syracuse University, 1-014 Center for Science & Technology, Syracuse, New York 13244-4100, United States
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30
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A test of improved force field parameters for urea: molecular-dynamics simulations of urea crystals. J Mol Model 2012; 18:3455-66. [DOI: 10.1007/s00894-011-1336-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 12/05/2011] [Indexed: 11/25/2022]
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31
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Kambara O, Takahashi K, Hayashi M, Kuo JL. Assessment of density functional theory to calculate the phase transition pressure of ice. Phys Chem Chem Phys 2012; 14:11484-90. [DOI: 10.1039/c2cp41495c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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32
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Mota OO, Çağın T. Anisotropic behavior of energetic materials at elevated pressure and temperature. J Loss Prev Process Ind 2011. [DOI: 10.1016/j.jlp.2011.06.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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33
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Erba A, Maschio L, Salustro S, Casassa S. A post-Hartree-Fock study of pressure-induced phase transitions in solid nitrogen: the case of the α, γ, and ε low-pressure phases. J Chem Phys 2011; 134:074502. [PMID: 21341854 DOI: 10.1063/1.3553206] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have performed fully periodic ab initio post-Hartree-Fock calculations on three low-temperature molecular phases of solid nitrogen, namely α, γ, and ε. The aim is to characterize the pressure-induced transitions among these phases, which are prototypical molecular crystals, through a periodic local-MP2 method, implemented in the CRYSCOR program. Cohesive energies are computed using extended correlation consistent molecular basis sets, up to quintuple-ζ quality. The MP2 description of equilibrium volumes, pressure-volume curves, and transition pressures is found to be in good agreement with the experiments.
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Affiliation(s)
- A Erba
- Dipartimento di Chimica IFM, Università di Torino, Torino, Italy.
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34
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King MD, Buchanan WD, Korter TM. Understanding the Terahertz Spectra of Crystalline Pharmaceuticals: Terahertz Spectroscopy and Solid-State Density Functional Theory Study of (S)-(+)-Ibuprofen and (RS)-Ibuprofen. J Pharm Sci 2011; 100:1116-29. [DOI: 10.1002/jps.22339] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 08/03/2010] [Accepted: 08/07/2010] [Indexed: 11/09/2022]
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35
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Ahmed Z, Chou SG, Siegrist K, Plusquellic DF. State-resolved THz spectroscopy and dynamics of crystalline peptide–water systems. Faraday Discuss 2011; 150:175-92; discussion 257-92. [DOI: 10.1039/c0fd00008f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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36
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King MD, Buchanan WD, Korter TM. Application of London-type dispersion corrections to the solid-state density functional theory simulation of the terahertz spectra of crystalline pharmaceuticals. Phys Chem Chem Phys 2011; 13:4250-9. [DOI: 10.1039/c0cp01595d] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Daramola DA, Singh D, Botte GG. Dissociation Rates of Urea in the Presence of NiOOH Catalyst: A DFT Analysis. J Phys Chem A 2010; 114:11513-21. [DOI: 10.1021/jp105159t] [Citation(s) in RCA: 174] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Damilola A. Daramola
- Department of Chemical and Biomolecular Engineering, Center for Electrochemical Engineering Research, Ohio University, Athens, Ohio 45701, United States
| | - Deepika Singh
- Department of Chemical and Biomolecular Engineering, Center for Electrochemical Engineering Research, Ohio University, Athens, Ohio 45701, United States
| | - Gerardine G. Botte
- Department of Chemical and Biomolecular Engineering, Center for Electrochemical Engineering Research, Ohio University, Athens, Ohio 45701, United States
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38
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Lo Presti L, Soave R, Longhi M, Ortoleva E. Conformational polymorphism in a Schiff-base macrocyclic organic ligand: an experimental and theoretical study. ACTA CRYSTALLOGRAPHICA SECTION B: STRUCTURAL SCIENCE 2010; 66:527-43. [PMID: 20841920 DOI: 10.1107/s0108768110029514] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Accepted: 07/23/2010] [Indexed: 11/11/2022]
Abstract
Polymorphism in the highly flexible organic Schiff-base macrocycle ligand 3,6,9,17,20,23-hexa-azapentacyclo(23.3.1.1(11,15).0(2,6).0(16,20))triaconta-1(29),9,11,13,15(30),23,25,27-octaene (DIEN, C(24)H(30)N(6)) has been studied by single-crystal X-ray diffraction and both solid-state and gas-phase density functional theory (DFT) calculations. In the literature, only solvated structures of the title compound are known. Two new polymorphs and a new solvated form of DIEN, all obtained from the same solvent with different crystallization conditions, are presented for the first time. They all have P\bar 1 symmetry, with the macrocycle positioned on inversion centres. The two unsolvated polymorphic forms differ in the number of molecules in the asymmetric unit Z', density and cohesive energy. Theoretical results confirm that the most stable form is (II°), with Z' = 1.5. Two distinct molecular conformations have been found, named `endo' or `exo' according to the orientation of the imine N atoms, which can be directed towards the interior or the exterior of the macrocycle. The endo arrangement is ubiquitous in the solid state and is shared by two independent molecules which constitute an invariant supramolecular synthon in all the known crystal forms of DIEN. It is also the most stable arrangement in the gas phase. The exo form, on the other hand, appears only in phase (II°), which contains both the conformers. Similarities and differences among the occurring packing motifs, as well as solvent effects, are discussed with the aid of Hirshfeld surface fingerprint plots and correlated to the results of the energy analysis. A possible interconversion path in the gas phase between the endo and the exo conformers has been found by DFT calculations; it consists of a two-step mechanism with activation energies of the order of 30-40 kJ mol(-1). These findings have been related to the empirical evidence that the most stable phase (II°) is also the last appearing one, in accordance with Ostwald's rule.
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Affiliation(s)
- Leonardo Lo Presti
- Dipartimento di Chimica Fisica ed Elettrochimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy.
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39
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40
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King MD, Buchanan WD, Korter TM. Investigating the Anharmonicity of Lattice Vibrations in Water-Containing Molecular Crystals through the Terahertz Spectroscopy of l-Serine Monohydrate. J Phys Chem A 2010; 114:9570-8. [DOI: 10.1021/jp105384x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Matthew D. King
- Department of Chemistry, Syracuse University, 1-014 Center for Science and Technology, Syracuse, New York 13244-4100
| | - William D. Buchanan
- Department of Chemistry, Syracuse University, 1-014 Center for Science and Technology, Syracuse, New York 13244-4100
| | - Timothy M. Korter
- Department of Chemistry, Syracuse University, 1-014 Center for Science and Technology, Syracuse, New York 13244-4100
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41
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King MD, Korter TM. Effect of Waters of Crystallization on Terahertz Spectra: Anhydrous Oxalic Acid and Its Dihydrate. J Phys Chem A 2010; 114:7127-38. [DOI: 10.1021/jp101935n] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Matthew D. King
- Department of Chemistry, Syracuse University, 1-014 Center for Science and Technology Syracuse, New York, 13244-4100
| | - Timothy M. Korter
- Department of Chemistry, Syracuse University, 1-014 Center for Science and Technology Syracuse, New York, 13244-4100
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42
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Cui G, Ding L, Feng F, Liu Y, Fang W. Insights into mechanistic photochemistry of urea. J Chem Phys 2010; 132:194308. [DOI: 10.1063/1.3397067] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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43
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Kong S, Shenderovich IG, Vener MV. Density functional study of the proton transfer effect on vibrations of strong (short) intermolecular O-H...N/O-...H-N+ hydrogen bonds in aprotic solvents. J Phys Chem A 2010; 114:2393-9. [PMID: 20104882 DOI: 10.1021/jp911694r] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structure and spectroscopic properties of the 1:1 complexes of substituted pyridines with benzoic acid and phenol derivatives in aprotic solvents are studied using B3LYP functional combined with the polarizable continuum model approximation. Two extreme structures are investigated: the state without (HB) and with proton transfer (PT). In the presence of an external electric field the O...N distance is contracted and the PT state does appear. The PT state of both the pyridine-benzoic and the pyridine-phenol complexes displays the only IR-active band in the 2800-1800 frequency region, which is located around 2000 cm(-1). However, the nature of the band is different for these two complexes. In the pyridine-benzoic acid complex it is practically a pure stretching vibration of the HN(+) group, while in the pyridine-phenol complex it is the mixed vibration of the bridging proton. A specific feature of the PT state in the pyridine-phenol complex is an IR-intensive band near 600 cm(-1), associated with the asymmetric stretching vibrations of the O(-)...HN(+) fragment. Its intensity is reciprocally proportional to the O...N distance. The appearance of this band provides an efficient criterion to differentiate between the HB and PT states of the 1:1 complexes of phenols with pyridines in aprotic solvents.
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Affiliation(s)
- Shushu Kong
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany
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44
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Tsuzuki S, Orita H, Honda K, Mikami M. First-Principles Lattice Energy Calculation of Urea and Hexamine Crystals by a Combination of Periodic DFT and MP2 Two-Body Interaction Energy Calculations. J Phys Chem B 2010; 114:6799-805. [DOI: 10.1021/jp912028q] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Seiji Tsuzuki
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568, Japan
| | - Hideo Orita
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568, Japan
| | - Kazumasa Honda
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568, Japan
| | - Masuhiro Mikami
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568, Japan
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45
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An improved generalized AMBER force field (GAFF) for urea. J Mol Model 2010; 16:1427-40. [DOI: 10.1007/s00894-010-0650-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Accepted: 12/22/2009] [Indexed: 10/19/2022]
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46
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Hermet P, Ghosez P. First-principles study of the dynamical and nonlinear optical properties of urea single crystals. Phys Chem Chem Phys 2010; 12:835-43. [DOI: 10.1039/b917347a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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47
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Jing YQ, Han KL. Quantum mechanical effect in protein–ligand interaction. Expert Opin Drug Discov 2009; 5:33-49. [DOI: 10.1517/17460440903440127] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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48
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Ferrero M, Civalleri B, Rérat M, Orlando R, Dovesi R. The calculation of the static first and second susceptibilities of crystalline urea: A comparison of Hartree–Fock and density functional theory results obtained with the periodic coupled perturbed Hartree–Fock/Kohn–Sham scheme. J Chem Phys 2009; 131:214704. [DOI: 10.1063/1.3267861] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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49
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Vener MV, Manaev AV, Hadzi D, Tsirelson VG. DFT Study of Proton Dynamics in the Potassium Hydrogen Maleate Crystal: the Infrared Versus the Inelastic Neutron Scattering Spectra. ACTA ACUST UNITED AC 2009. [DOI: 10.1524/zpch.2008.5394] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Abstract
The structure, harmonic frequencies and infrared (IR) intensities of the fundamental transitions in potassium hydrogen maleate (KHM) crystal have been computed using the BLYP/6-31G** method with periodic boundary conditions. The inelastic neutron scattering (INS) intensities of the fundamental transitions were evaluated and compared with the experimental INS spectra of hydrogenated sample and isotopic analogues of the KHM crystal; the agreement is reasonable good. Spectroscopic manifestations of the proton dynamics in the strong intramolecular H-bond were clarified by comparison of the computed frequencies of the IR and INS-active fundamental transitions. Due to several reasons, the number of the bands and their relative intensity were found to differ between the INS and IR spectra of the KHM crystal. Reduced masses for the asymmetric O…H…O stretching vibrations of the hydrogen maleate ion appear to be larger 1 a.m.u. because of the strong coupling between the bridging proton motion and the various intramolecular vibrations.
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50
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Lo Presti L, Ellern A, Destro R, Lunelli B. Effect of Methoxy Substituents on the Structural and Electronic Properties of Fluorinated Cyclobutenes: A Study of Hexafluorocyclobutene and Its Vinyl Methoxy Derivatives by XRD and Periodic DFT Calculations. J Phys Chem A 2009; 113:3186-96. [DOI: 10.1021/jp8084809] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Leonardo Lo Presti
- Dipartimento di Chimica Fisica ed Elettrochimica, Università di Milano, Via Golgi 19, 20133 Milano, Italy, Chemistry Department, Iowa State University, 1711 Gilman Hall, Ames, Iowa 50011, and Istituto per lo Studio dei Materiali Nanostrutturati (ISMN) CNR, Via P.Gobetti, 101, 40129 Bologna, Italy
| | - Arkady Ellern
- Dipartimento di Chimica Fisica ed Elettrochimica, Università di Milano, Via Golgi 19, 20133 Milano, Italy, Chemistry Department, Iowa State University, 1711 Gilman Hall, Ames, Iowa 50011, and Istituto per lo Studio dei Materiali Nanostrutturati (ISMN) CNR, Via P.Gobetti, 101, 40129 Bologna, Italy
| | - Riccardo Destro
- Dipartimento di Chimica Fisica ed Elettrochimica, Università di Milano, Via Golgi 19, 20133 Milano, Italy, Chemistry Department, Iowa State University, 1711 Gilman Hall, Ames, Iowa 50011, and Istituto per lo Studio dei Materiali Nanostrutturati (ISMN) CNR, Via P.Gobetti, 101, 40129 Bologna, Italy
| | - Bruno Lunelli
- Dipartimento di Chimica Fisica ed Elettrochimica, Università di Milano, Via Golgi 19, 20133 Milano, Italy, Chemistry Department, Iowa State University, 1711 Gilman Hall, Ames, Iowa 50011, and Istituto per lo Studio dei Materiali Nanostrutturati (ISMN) CNR, Via P.Gobetti, 101, 40129 Bologna, Italy
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