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1.  Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D) 
The accuracy of 215 experimental organic crystal structures from powder diffraction data is validated against a dispersion-corrected density functional theory method.
In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom.
doi:10.1107/S2052520614022902
PMCID: PMC4468513  PMID: 25449625
dispersion-corrected density functional theory; powder data validation; energy mimimization
2.  Distinguishing tautomerism in the crystal structure of (Z)-N-(5-ethyl-2,3-di­hydro-1,3,4-thia­diazol-2-yl­idene)-4-methyl­benzene­sulfonamide using DFT-D calculations and 13C solid-state NMR 
The crystal structure of (Z)-N-(5-ethyl-2,3-di­hydro-1,3,4-thia­diazol-2-yl­idene)-4-methyl­benzene­sulfonamide contains an imine tautomer, rather than the previously reported amine tautomer. The tautomers can be distinguished using dispersion-corrected density functional theory calculations and by comparison of calculated and measured 13C solid-state NMR spectra.
The crystal structure of the title compound, C11H13N3O2S2, has been determined previously on the basis of refinement against laboratory powder X-ray diffraction (PXRD) data, supported by comparison of measured and calculated 13C solid-state NMR spectra [Hangan et al. (2010 ▶). Acta Cryst. B66, 615–621]. The mol­ecule is tautomeric, and was reported as an amine tautomer [systematic name: N-(5-ethyl-1,3,4-thia­diazol-2-yl)-p-toluene­sulfonamide], rather than the correct imine tautomer. The protonation site on the mol­ecule’s 1,3,4-thia­diazole ring is indicated by the inter­molecular contacts in the crystal structure: N—H⋯O hydrogen bonds are established at the correct site, while the alternative protonation site does not establish any notable inter­molecular inter­actions. The two tautomers provide essentially identical Rietveld fits to laboratory PXRD data, and therefore they cannot be directly distinguished in this way. However, the correct tautomer can be distinguished from the incorrect one by previously reported qu­anti­tative criteria based on the extent of structural distortion on optimization of the crystal structure using dispersion-corrected density functional theory (DFT-D) calculations. Calculation of the 13C SS-NMR spectrum based on the correct imine tautomer also provides considerably better agreement with the measured 13C SS-NMR spectrum.
doi:10.1107/S2053229614015356
PMCID: PMC4174016  PMID: 25093360
crystal structure; powder diffraction; NMR analysis; amine–imine tautomerism; dispersion-corrected DFT
3.  The active site of hen egg-white lysozyme: flexibility and chemical bonding 
Chemical bonding at the active site of lysozyme is analyzed on the basis of a multipole model employing transferable multipole parameters from a database. Large B factors at low temperatures reflect frozen-in disorder, but therefore prevent a meaningful free refinement of multipole parameters.
Chemical bonding at the active site of hen egg-white lysozyme (HEWL) is analyzed on the basis of Bader’s quantum theory of atoms in molecules [QTAIM; Bader (1994 ▶), Atoms in Molecules: A Quantum Theory. Oxford University Press] applied to electron-density maps derived from a multipole model. The observation is made that the atomic displacement parameters (ADPs) of HEWL at a temperature of 100 K are larger than ADPs in crystals of small biological molecules at 298 K. This feature shows that the ADPs in the cold crystals of HEWL reflect frozen-in disorder rather than thermal vibrations of the atoms. Directly generalizing the results of multipole studies on small-molecule crystals, the important consequence for electron-density analysis of protein crystals is that multipole parameters cannot be independently varied in a meaningful way in structure refinements. Instead, a multipole model for HEWL has been developed by refinement of atomic coordinates and ADPs against the X-ray diffraction data of Wang and coworkers [Wang et al. (2007), Acta Cryst. D63, 1254–1268], while multipole parameters were fixed to the values for transferable multipole parameters from the ELMAM2 database [Domagala et al. (2012), Acta Cryst. A68, 337–351] . Static and dynamic electron densities based on this multipole model are presented. Analysis of their topological properties according to the QTAIM shows that the covalent bonds possess similar properties to the covalent bonds of small molecules. Hydrogen bonds of intermediate strength are identified for the Glu35 and Asp52 residues, which are considered to be essential parts of the active site of HEWL. Furthermore, a series of weak C—H⋯O hydrogen bonds are identified by means of the existence of bond critical points (BCPs) in the multipole electron density. It is proposed that these weak interactions might be important for defining the tertiary structure and activity of HEWL. The deprotonated state of Glu35 prevents a distinction between the Phillips and Koshland mechanisms.
doi:10.1107/S1399004714001928
PMCID: PMC3975892  PMID: 24699657
hen egg-white lysozyme; multipole model; multipole parameters
4.  Structure of Pigment Yellow 181 dimethylsulfoxide N-methyl-2-pyrrolidone (1:1:1) solvate from XRPD + DFT-D 
The relatively complex structure of a triclinic disolvate was solved from low-resolution laboratory powder diffraction data through the intermediate use of dummy atoms and the combination with quantum-mechanical calculations.
With only a 2.6 Å resolution laboratory powder diffraction pattern of the θ phase of Pigment Yellow 181 (P.Y. 181) available, crystal-structure solution and Rietveld refinement proved challenging; especially when the crystal structure was shown to be a triclinic dimethylsulfoxide N-methyl-2-pyrrolidone (1:1:1) solvate. The crystal structure, which in principle has 28 possible degrees of freedom, was determined in three stages by a combination of simulated annealing, partial Rietveld refinement with dummy atoms replacing the solvent molecules and further simulated annealing. The θ phase not being of commercial interest, additional experiments were not economically feasible and additional dispersion-corrected density functional theory (DFT-D) calculations were employed to confirm the correctness of the crystal structure. After the correctness of the structure had been ascertained, the bond lengths and valence angles from the DFT-D minimized crystal structure were fed back into the Rietveld refinement as geometrical restraints (‘polymorph-dependent restraints’) to further improve the details of the crystal structure; the positions of the H atoms were also taken from the DFT-D calculations. The final crystal structure is a layered structure with an elaborate network of hydrogen bonds.
doi:10.1107/S2052520615000724
PMCID: PMC4316649  PMID: 25643720
Pigment Yellow 181; X-ray powder diffraction; dispersion-corrected density functional theory
5.  Structural basis for the transformation pathways of the sodium naproxen anhydrate–hydrate system 
IUCrJ  2014;1(Pt 5):328-337.
Relationships between the crystal structures of two polymorphs of sodium naproxen dihydrate and its monohydrate and anhydrate phases provide a basis to rationalize the observed transformation pathways in the sodium (S)-naproxen anhydrate–hydrate system.
Crystal structures are presented for two dihydrate polymorphs (DH-I and DH-II) of the non-steroidal anti-inflammatory drug sodium (S)-naproxen. The structure of DH-I is determined from twinned single crystals obtained by solution crystallization. DH-II is obtained by solid-state routes, and its structure is derived using powder X-ray diffraction, solid-state 13C and 23Na MAS NMR, and molecular modelling. The validity of both structures is supported by dispersion-corrected density functional theory (DFT-D) calculations. The structures of DH-I and DH-II, and in particular their relationships to the monohydrate (MH) and anhydrate (AH) structures, provide a basis to rationalize the observed transformation pathways in the sodium (S)-naproxen anhydrate–hydrate system. All structures contain Na+/carboxylate/H2O sections, alternating with sections containing the naproxen molecules. The structure of DH-I is essentially identical to MH in the naproxen region, containing face-to-face arrangements of the naphthalene rings, whereas the structure of DH-II is comparable to AH in the naproxen region, containing edge-to-face arrangements of the naphthalene rings. This structural similarity permits topotactic transformation between AH and DH-II, and between MH and DH-I, but requires re-organization of the naproxen molecules for transformation between any other pair of structures. The topotactic pathways dominate at room temperature or below, while the non-topotactic pathways become active at higher temperatures. Thermochemical data for the dehydration processes are rationalized in the light of this new structural information.
doi:10.1107/S2052252514015450
PMCID: PMC4174875  PMID: 25295174
pharmaceutical; hydrate; X-ray diffraction; solid-state NMR; DFT-D
6.  Effects of Vacancy Cluster Defects on Electrical and Thermodynamic Properties of Silicon Crystals 
The Scientific World Journal  2014;2014:863404.
A first-principle plane-wave pseudopotential method based on the density function theory (DFT) was employed to investigate the effects of vacancy cluster (VC) defects on the band structure and thermoelectric properties of silicon (Si) crystals. Simulation results showed that various VC defects changed the energy band and localized electron density distribution of Si crystals and caused the band gap to decrease with increasing VC size. The results can be ascribed to the formation of a defect level produced by the dangling bonds, floating bonds, or high-strain atoms surrounding the VC defects. The appearance of imaginary frequencies in the phonon spectrum of defective Si crystals indicates that the defect-region structure is dynamically unstable and demonstrates phase changes. The phonon dispersion relation and phonon density of state were also investigated using density functional perturbation theory. The obtained Debye temperature (θD) for a perfect Si crystal had a minimum value of 448 K at T = 42 K and a maximum value of 671 K at the high-temperature limit, which is consistent with the experimental results reported by Flubacher. Moreover, the Debye temperature decreased with increases in the VC size. VC defects had minimal effects on the heat capacity (Cv) value when temperatures were below 150 K. As the temperature was higher than 150 K, the heat capacity gradually increased with increasing temperature until it achieved a constant value of 11.8 cal/cell·K. The heat capacity significantly decreased as the VC size increased. For a 2 × 2 × 2 superlattice Si crystal containing a hexagonal ring VC (HRVC10), the heat capacity decreased by approximately 17%.
doi:10.1155/2014/863404
PMCID: PMC3913515  PMID: 24526923
7.  Crystal structure of lead(II) tartrate: a redetermination 
The redetermination of the crystal structure of lead tartrate from crystals grown in a gel medium confirmed the previous powder X-ray diffraction study in the space group P212121 with higher precision. Contradictions in the literature regarding space group and water content could be clarified.
Single crystals of poly[μ4-tartrato-κ6 O 1,O 3:O 1′:O 2,O 4:O 4′-lead], [Pb(C4H4O6)]n, were grown in a gel medium. In comparison with the previous structure determination of this compound from laboratory powder X-ray diffraction data [De Ridder et al. (2002 ▶). Acta Cryst. C58, m596–m598], the redetermination on the basis of single-crystal data reveals the absolute structure, all atoms with anisotropic displacement parameters and a much higher accuracy in terms of bond lengths and angles. It could be shown that a different space group or incorporation of water as reported for similarly gel-grown lead tartrate crystals is incorrect. In the structure, each Pb2+ cation is bonded to eight O atoms of five tartrate anions, while each tartrate anion links four Pb2+ cations. The resulting three-dimensional framework is stabilized by O—H⋯O hydrogen bonds between the OH groups of one tartrate anion and the carboxyl­ate O atoms of adjacent anions.
doi:10.1107/S2056989014027376
PMCID: PMC4331892  PMID: 25705458
crystal structure; lead tartrate; gel growth; redetermination; O—H⋯O hydrogen bonds
8.  Redetermination of Zn2Mo3O8  
The crystal structure of dizinc trimolybdenum(IV) octa­oxide, Zn2Mo3O8, has been redetermined from single-crystal X-ray data. The structure has been reported previously based on neutron powder diffraction data [Hibble et al. (1999 ▶). Acta Cryst. B55, 683-697] and single-crystal data [McCarroll et al. (1957 ▶). J. Am. Chem. Soc. 79, 5410–5414; Ansell & Katz (1966 ▶) Acta Cryst. 21, 482–485]. The results of the current redetermination show an improvement in the precision of the structural and geometric parameters with all atoms refined with anisotropic displacement parameters. The crystal structure consists of distorted hexa­gonal-close-packed oxygen layers with stacking sequence abac along [001] and is held together by alternating zinc and molybdenum layers. The Zn atoms occupy both tetra­hedral and octa­hedral inter­stices with a ratio of 1:1. The Mo atoms occupy octa­hedral sites and form strongly bonded triangular clusters involving three MoO6 octa­hedra that are each shared along two edges, forming a Mo3O13 unit. All atoms lie on special positions. The Zn atoms are in 2b Wyckoff positions with 3m. site symmetry, the Mo atoms are in 6c Wyckoff positions with . m. site symmetry and the O atoms are in 2a, 2b and 6c Wyckoff positions with 3m. and . m. site symmetries, respectively.
doi:10.1107/S1600536809021928
PMCID: PMC2969349  PMID: 21582645
9.  Anharmonicity and isomorphic phase transition: a multi-temperature X-ray single-crystal and powder diffraction study of 1-(2′-aminophenyl)-2-methyl-4-nitroimidazole 
Iucrj  2014;1(Pt 2):110-118.
Multi-temperature single-crystal and powder diffraction experiments on 1-(2′-aminophenyl)-2-methyl-4-nitroimidazole show that this crystal undergoes an isomorphic phase transition with the coexistence of two phase domains over a wide temperature range. The anharmonic approach was the only way to model the resulting disorder.
The harmonic model of atomic nuclear motions is usually enough for multipole modelling of high-resolution X-ray diffraction data; however, in some molecular crystals, such as 1-(2′-aminophenyl)-2-methyl-4-nitro-1H-imidazole [Paul, Kubicki, Jelsch et al. (2011 ▶). Acta Cryst. B67, 365–378], it may not be sufficient for a correct description of the charge-density distribution. Multipole refinement using harmonic atom vibrations does not lead to the best electron density model in this case and the so-called ‘shashlik-like’ pattern of positive and negative residual electron density peaks is observed in the vicinity of some atoms. This slight disorder, which cannot be modelled by split atoms, was solved using third-order anharmonic nuclear motion (ANM) parameters. Multipole refinement of the experimental high-resolution X-ray diffraction data of 1-(2′-aminophenyl)-2-methyl-4-nitro-1H-imidazole at three different temperatures (10, 35 and 70 K) and a series of powder diffraction experiments (20 ≤ T ≤ 300 K) were performed to relate this anharmonicity observed for several light atoms (N atoms of amino and nitro groups, and O atoms of nitro groups) to an isomorphic phase transition reflected by a change in the b cell parameter around 65 K. The observed disorder may result from the coexistence of domains of two phases over a large temperature range, as shown by low-temperature powder diffraction.
doi:10.1107/S2052252514002838
PMCID: PMC4062092  PMID: 25075327
anharmonicity; isomorphic phase transition; experimental charge density; X-ray closed-circuit helium cryostat; Hansen–Coppens model; multiple-temperature powder diffraction
10.  Accurate and efficient representation of intra­molecular energy in ab initio generation of crystal structures. I. Adaptive local approximate models 
This article describes an important improvement in the CrystalPredictor II code: adaptive Local Approximate Models (LAMs). This improvement allows the most efficient use of computational effort to cover a flexible molecule’s conformational space, and is illustrated with a crystal structure prediction (CSP) investigation into the sixth blind test molecule 26.
The global search stage of crystal structure prediction (CSP) methods requires a fine balance between accuracy and computational cost, particularly for the study of large flexible molecules. A major improvement in the accuracy and cost of the intramolecular energy function used in the CrystalPredictor II [Habgood et al. (2015 ▸). J. Chem. Theory Comput. 11, 1957–1969] program is presented, where the most efficient use of computational effort is ensured via the use of adaptive local approximate model (LAM) placement. The entire search space of the relevant molecule’s conformations is initially evaluated using a coarse, low accuracy grid. Additional LAM points are then placed at appropriate points determined via an automated process, aiming to minimize the computational effort expended in high-energy regions whilst maximizing the accuracy in low-energy regions. As the size, complexity and flexibility of molecules increase, the reduction in computational cost becomes marked. This improvement is illustrated with energy calculations for benzoic acid and the ROY molecule, and a CSP study of molecule (XXVI) from the sixth blind test [Reilly et al. (2016 ▸). Acta Cryst. B72, 439–459], which is challenging due to its size and flexibility. Its known experimental form is successfully predicted as the global minimum. The computational cost of the study is tractable without the need to make unphysical simplifying assumptions.
doi:10.1107/S2052520616015122
PMCID: PMC5134761  PMID: 27910837
crystal structure prediction; solid-state science; local apprioximate model
11.  Polarizable atomic multipole X-ray refinement: application to peptide crystals 
A method to accelerate the computation of structure factors from an electron density described by anisotropic and aspherical atomic form factors via fast Fourier transformation is described for the first time.
Recent advances in computational chemistry have produced force fields based on a polarizable atomic multipole description of biomolecular electrostatics. In this work, the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field is applied to restrained refinement of molecular models against X-ray diffraction data from peptide crystals. A new formalism is also developed to compute anisotropic and aspherical structure factors using fast Fourier transformation (FFT) of Cartesian Gaussian multipoles. Relative to direct summation, the FFT approach can give a speedup of more than an order of magnitude for aspherical refinement of ultrahigh-resolution data sets. Use of a sublattice formalism makes the method highly parallelizable. Application of the Cartesian Gaussian multipole scattering model to a series of four peptide crystals using multipole coefficients from the AMOEBA force field demonstrates that AMOEBA systematically underestimates electron density at bond centers. For the trigonal and tetrahedral bonding geometries common in organic chemistry, an atomic multipole expansion through hexadecapole order is required to explain bond electron density. Alternatively, the addition of inter­atomic scattering (IAS) sites to the AMOEBA-based density captured bonding effects with fewer parameters. For a series of four peptide crystals, the AMOEBA–IAS model lowered R free by 20–40% relative to the original spherically symmetric scattering model.
doi:10.1107/S0907444909022707
PMCID: PMC2733883  PMID: 19690373
scattering factors; aspherical; anisotropic; force fields; multipole; polarization; AMOEBA; bond density; direct summation; FFT; SGFFT; Ewald; PME
12.  A machine learning correction for DFT non-covalent interactions based on the S22, S66 and X40 benchmark databases 
Background
Non-covalent interactions (NCIs) play critical roles in supramolecular chemistries; however, they are difficult to measure. Currently, reliable computational methods are being pursued to meet this challenge, but the accuracy of calculations based on low levels of theory is not satisfactory and calculations based on high levels of theory are often too costly. Accordingly, to reduce the cost and increase the accuracy of low-level theoretical calculations to describe NCIs, an efficient approach is proposed to correct NCI calculations based on the benchmark databases S22, S66 and X40 (Hobza in Acc Chem Rev 45: 663–672, 2012; Řezáč et al. in J Chem Theory Comput 8:4285, 2012).
Results
A novel type of NCI correction is presented for density functional theory (DFT) methods. In this approach, the general regression neural network machine learning method is used to perform the correction for DFT methods on the basis of DFT calculations. Various DFT methods, including M06-2X, B3LYP, B3LYP-D3, PBE, PBE-D3 and ωB97XD, with two small basis sets (i.e., 6-31G* and 6-31+G*) were investigated. Moreover, the conductor-like polarizable continuum model with two types of solvents (i.e., water and pentylamine, which mimics a protein environment with ε = 4.2) were considered in the DFT calculations. With the correction, the root mean square errors of all DFT calculations were improved by at least 70 %. Relative to CCSD(T)/CBS benchmark values (used as experimental NCI values because of its high accuracy), the mean absolute error of the best result was 0.33 kcal/mol, which is comparable to high-level ab initio methods or DFT methods with fairly large basis sets. Notably, this level of accuracy is achieved within a fraction of the time required by other methods. For all of the correction models based on various DFT approaches, the validation parameters according to OECD principles (i.e., the correlation coefficient R2, the predictive squared correlation coefficient q2 and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$q_{cv}^{2}$$\end{document}qcv2 from cross-validation) were >0.92, which suggests that the correction model has good stability, robustness and predictive power.
Conclusions
The correction can be added following DFT calculations. With the obtained molecular descriptors, the NCIs produced by DFT methods can be improved to achieve high-level accuracy. Moreover, only one parameter is introduced into the correction model, which makes it easily applicable. Overall, this work demonstrates that the correction model may be an alternative to the traditional means of correcting for NCIs.Graphical abstractA machine learning correction model efficiently improved the accuracy of non-covalent interactions(NCIs) calculated by DFT methods. The application of the correction model is easy and flexible, so it may be an alternative correction means for NCIs by first-principle calculations.
Electronic supplementary material
The online version of this article (doi:10.1186/s13321-016-0133-7) contains supplementary material, which is available to authorized users.
doi:10.1186/s13321-016-0133-7
PMCID: PMC4855356  PMID: 27148408
Non-covalent interactions; Density functional theory; Machine learning correction; Computational accuracy; Feature selection
13.  Structural and spectral investigations of the recently synthesized chalcone (E)-3-mesityl-1-(naphthalen-2-yl) prop-2-en-1-one, a potential chemotherapeutic agent 
Background
Chalcones (1,3-diaryl-2-propen-1-ones, represent an important subgroup of the polyphenolic family, which have shown a wide spectrum of medical and industrial application. Due to their redundancy in plants and ease of preparation, this category of molecules has inspired considerable attention for potential therapeutic uses. They are also effective in vivo as anti-tumor promoting, cell proliferating inhibitors and chemo preventing agents.
Results
Synthesis and molecular structure investigation of (E)-3-mesityl-1-(naphthalen-2-yl) prop-2-en-1-one (3) is reported. The structure of the title compound 3 is confirmed by X-ray crystallography. The optimized molecular structure of the studied compound is calculated using DFT B3LYP/6-311G (d,p) method. The calculated geometric parameters are in good agreement with the experimental data obtained from our reported X-ay structure. The calculated IR fundamental bands were assigned and compared with the experimental data. The electronic spectra of the studied compound have been calculated using the time dependant density functional theory (TD-DFT). The longest wavelength band is due to H → L (79 %) electronic transition which belongs to π-π* excitation. The 1H- and 13C-NMR chemical shifts were calculated using gauge independent atomic orbitals (GIAO) method, which showed good correlations with the experimental data (R2 = 0.9911–0.9965). The natural bond orbital (NBO) calculations were performed to predict the natural atomic charges at different atomic sites. The molecular electrostatic potential (MEP) was used to visualize the charge distribution on the molecule. Molecular docking results suggest that the compound might exhibit inhibitory activity against GPb and may act as potential anti-diabetic compound.
Conclusions
(E)-3-Mesityl-1-(naphthalen-2-yl) prop-2-en-1-one single crystal is grown and characterized by single crystal X-ray diffraction, FT-IR, UV–vis, DFT and optimized geometrical parameters are close to the experimental bond lengths and angles. Molecular stability was successfully analyzed using NBO and electron delocalization is confirmed by MEP. Prediction of Activity Spectra Analysis of the title compound, predicts anti-diabetic activity with probability to have an active value of 0.348.
Graphical Abstract(E)-3-Mesityl-1-(naphthalen-2-yl) prop-2-en-1-one: a crystal structure and computational studies.
Electronic supplementary material
The online version of this article (doi:10.1186/s13065-015-0112-5) contains supplementary material, which is available to authorized users.
doi:10.1186/s13065-015-0112-5
PMCID: PMC4477317  PMID: 26106444
Aldol product; Chalcone; X-Ray; DFT compution; PAAS
14.  Structural and spectral investigations of the recently synthesized chalcone (E)-3-mesityl-1-(naphthalen-2-yl) prop-2-en-1-one, a potential chemotherapeutic agent 
Background
Chalcones (1,3-diaryl-2-propen-1-ones, represent an important subgroup of the polyphenolic family, which have shown a wide spectrum of medical and industrial application. Due to their redundancy in plants and ease of preparation, this category of molecules has inspired considerable attention for potential therapeutic uses. They are also effective in vivo as anti-tumor promoting, cell proliferating inhibitors and chemo preventing agents.
Results
Synthesis and molecular structure investigation of (E)-3-mesityl-1-(naphthalen-2-yl) prop-2-en-1-one (3) is reported. The structure of the title compound 3 is confirmed by X-ray crystallography. The optimized molecular structure of the studied compound is calculated using DFT B3LYP/6-311G (d,p) method. The calculated geometric parameters are in good agreement with the experimental data obtained from our reported X-ay structure. The calculated IR fundamental bands were assigned and compared with the experimental data. The electronic spectra of the studied compound have been calculated using the time dependant density functional theory (TD-DFT). The longest wavelength band is due to H → L (79 %) electronic transition which belongs to π-π* excitation. The 1H- and 13C-NMR chemical shifts were calculated using gauge independent atomic orbitals (GIAO) method, which showed good correlations with the experimental data (R2 = 0.9911–0.9965). The natural bond orbital (NBO) calculations were performed to predict the natural atomic charges at different atomic sites. The molecular electrostatic potential (MEP) was used to visualize the charge distribution on the molecule. Molecular docking results suggest that the compound might exhibit inhibitory activity against GPb and may act as potential anti-diabetic compound.
Conclusions
(E)-3-Mesityl-1-(naphthalen-2-yl) prop-2-en-1-one single crystal is grown and characterized by single crystal X-ray diffraction, FT-IR, UV–vis, DFT and optimized geometrical parameters are close to the experimental bond lengths and angles. Molecular stability was successfully analyzed using NBO and electron delocalization is confirmed by MEP. Prediction of Activity Spectra Analysis of the title compound, predicts anti-diabetic activity with probability to have an active value of 0.348.
Graphical Abstract(E)-3-Mesityl-1-(naphthalen-2-yl) prop-2-en-1-one: a crystal structure and computational studies.
Electronic supplementary material
The online version of this article (doi:10.1186/s13065-015-0112-5) contains supplementary material, which is available to authorized users.
doi:10.1186/s13065-015-0112-5
PMCID: PMC4477317  PMID: 26106444
Aldol product; Chalcone; X-Ray; DFT compution; PAAS
15.  Hirshfeld atom refinement 
IUCrJ  2014;1(Pt 5):361-379.
The new automated iterative Hirshfeld atom refinement method is explained and validated through comparison of structural models of Gly–l-Ala obtained from synchrotron X-ray and neutron diffraction data at 12, 50, 150 and 295 K. Structural parameters involving hydrogen atoms are determined with comparable precision from both experiments and agree mostly to within two combined standard uncertainties.
Hirshfeld atom refinement (HAR) is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-made ab initio quantum mechanical molecular electron densities without any further approximation. Here the original HAR method is extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares refinements, repeated until convergence. The importance of this iterative procedure is illustrated via the example of crystalline ammonia. The new HAR method is then applied to X-ray diffraction data of the dipeptide Gly–l-Ala measured at 12, 50, 100, 150, 220 and 295 K, using Hartree–Fock and BLYP density functional theory electron densities and three different basis sets. All positions and anisotropic displacement parameters (ADPs) are freely refined without constraints or restraints – even those for hydrogen atoms. The results are systematically compared with those from neutron diffraction experiments at the temperatures 12, 50, 150 and 295 K. Although non-hydrogen-atom ADPs differ by up to three combined standard uncertainties (csu’s), all other structural parameters agree within less than 2 csu’s. Using our best calculations (BLYP/cc-pVTZ, recommended for organic molecules), the accuracy of determining bond lengths involving hydrogen atoms from HAR is better than 0.009 Å for temperatures of 150 K or below; for hydrogen-atom ADPs it is better than 0.006 Å2 as judged from the mean absolute X-ray minus neutron differences. These results are among the best ever obtained. Remarkably, the precision of determining bond lengths and ADPs for the hydrogen atoms from the HAR procedure is comparable with that from the neutron measurements – an outcome which is obtained with a routinely achievable resolution of the X-ray data of 0.65 Å.
doi:10.1107/S2052252514014845
PMCID: PMC4174878  PMID: 25295177
aspherical atom partitioning; quantum mechanical molecular electron densities; X-ray structure refinement; hydrogen atom modelling; anisotropic displacement parameters
16.  The Catalytic Mn2+ Sites in the Enolase-Inhibitor Complex - Crystallography, Single Crystal EPR and DFT Calculations 
Crystals of Zn2+ / Mn2+ yeast enolase with the inhibitor PhAH (phosphonoacetohydroxamate) were grown under conditions with a slight preference for binding of Zn2+ at the higher affinity site, site I. The structure of the Zn2+/Mn2+ PhAH complex was solved at a resolution of 1.54 Å and the two catalytic metal binding sites, I and II, show only subtle displacement compared to that of the corresponding complex with the native Mg2+ ions. Low temperature echo-detected high field (W-band, 95 GHz) EPR (electron paramagnetic resonance) and 1H ENDOR (electron-nuclear double resonance) were carried out on a single crystal and rotation patterns were acquired in two perpendicular planes. Analysis of the rotation patterns resolved a total of six Mn2+sites; four symmetry related sites of one type and two out of the four of the other type. The observation of two chemically inequivalent Mn2+ sites shows that Mn2+ ions populates both site I and II and the zero-field splitting ( ZFS) tensors of the Mn2+ in the two sites were determined. The Mn2+site with the larger D-value was assigned to site I based on the 1H ENDOR spectra, which identified the relevant water ligands. This assignment is consistent with the seemingly larger deviation of site I from octahedral symmetry, compared to site II. The ENDOR results gave the coordinates of the protons of two water ligands and adding them to the crystal structure revealed their involvement in a network of H-bonds stabilizing the binding of the metal ions and PhAH. Although specific hyperfine interactions with the inhibitor were not determined, the spectroscopic properties of the Mn2+ in the two sites were consistent with the crystal structure. Density functional theory (DFT) calculations carried out on a cluster representing the catalytic site, with Mn2+ in site I and Zn2+ in site II, and vice versa, gave overestimated D values on the order of the experimental ones, although the larger D value was found for Mn2+ in site II rather than in site I. This was attributed to the high sensitivity of the ZFS parameters to the Mn-O bond lengths and orientations, such that small, but significant differences between the optimized and crystal structure alter the ZFS considerably, well above the difference between the two sites.
doi:10.1021/ja066124e
PMCID: PMC2538446  PMID: 17367133
17.  CHARMM Additive All-Atom Force Field for Aldopentofuranoses, Methyl-Aldopentofuranosides and Fructofuranose 
The journal of physical chemistry. B  2009;113(37):12466-12476.
An additive all-atom empirical force field for aldopentofuranoses, methyl-aldopentofuranosides (Me-aldopentofuranosides) and fructofuranose carbohydrates, compatible with existing CHARMM carbohydrate parameters, is presented. Building on existing parameters transferred from cyclic ethers and hexopyranoses, parameters were further developed using target data for complete furanose carbohydrates as well as O-methyl tetrahydrofuran. The bond and angle equilibrium parameters were adjusted to reproduce target geometries from a survey of furanose crystal structures, and dihedral parameters were fit to over 1700 quantum mechanical (QM) MP2/cc-pVTZ//MP2/6-31G(d) conformational energies. The conformational energies were for a variety of complete furanose monosaccharides, and included two-dimensional ring pucker energy surfaces. Bonded parameter optimization led to the correct description of the ring pucker for a large set of furanose compounds, while furanose-water interaction energies and distances reproduced QM HF/6-31G(d) results for a number of furanose monosaccharides, thereby validating the nonbonded parameters. Crystal lattice unit cell parameters and volumes, aqueous-phase densities, and aqueous NMR ring pucker and exocyclic data were used to validate the parameters in condensed-phase environments. Conformational sampling analysis of the ring pucker and exocyclic group showed excellent agreement with experimental NMR data, demonstrating that the conformational energetics in aqueous solution are accurately described by the optimized force field. Overall, the parameters reproduce available experimental data well and are anticipated to be of utility in future computational studies of carbohydrates, including in the context of proteins, nucleic acids and/or lipids when combined with existing CHARMM biomolecular force fields.
doi:10.1021/jp905496e
PMCID: PMC2741538  PMID: 19694450
furanose; furanoside; aldopentose; carbohydrates; ribose; arabinose; fructose; empirical force field
18.  Redetermined structure of gossypol (P3 polymorph) 
An improved crystal structure of the title compound, C30H30O8 (systematic name: 1,1′,6,6′,7,7′-hexa­hydroxy-5,5′-diisopropyl-3,3′-dimeth­yl[2,2′-bi­naphthalene]-8,8′-dicarbaldehyde), was determined based on modern CCD data. Compared to the previous structure [Talipov et al. (1985). Khim. Prirod. Soedin. (Chem. Nat. Prod.), 6, 20–24], geometrical precision has been improved (typical C—C bond-distance s.u. = 0.002 Å in the present structure compared to 0.005 Å in the previous structure) and the locations of several H atoms have been corrected. The gossypol mol­ecules are in the aldehyde tautomeric form and the dihedral angle between the naphthyl fragments is 80.42 (4)°. Four intra­molecular O—H⋯O hydrogen bonds are formed. In the crystal, inversion dimers with graph-set motif R 2 2(20) are formed by pairs of O—H⋯O hydrogen bonds; another pair of O—H⋯O hydrogen bonds with the same graph-set motif links the dimers into [001] chains. The packing of such chains in the crystal leads to the formation of channels (diameter = 5–8 Å) propagating in the [101] direction. The channels presumably contain highly disordered solvent mol­ecules; their contribution to the scattering was removed with the SQUEEZE [Spek (2015). Acta Cryst. C71, 9–18] routine in PLATON and the stated mol­ecular mass, density etc., do not take them into account.
doi:10.1107/S205698901500941X
PMCID: PMC4518924  PMID: 26279897
crystal structure; redetermination; gossypol; polymorph; hydrogen bonding
19.  Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations 
We have estimated the binding affinity of three sets of ligands of the heat-shock protein 90 in the D3R grand challenge blind test competition. We have employed four different methods, based on five different crystal structures: first, we docked the ligands to the proteins with induced-fit docking with the Glide software and calculated binding affinities with three energy functions. Second, the docked structures were minimised in a continuum solvent and binding affinities were calculated with the MM/GBSA method (molecular mechanics combined with generalised Born and solvent-accessible surface area solvation). Third, the docked structures were re-optimised by combined quantum mechanics and molecular mechanics (QM/MM) calculations. Then, interaction energies were calculated with quantum mechanical calculations employing 970–1160 atoms in a continuum solvent, combined with energy corrections for dispersion, zero-point energy and entropy, ligand distortion, ligand solvation, and an increase of the basis set to quadruple-zeta quality. Fourth, relative binding affinities were estimated by free-energy simulations, using the multi-state Bennett acceptance-ratio approach. Unfortunately, the results were varying and rather poor, with only one calculation giving a correlation to the experimental affinities larger than 0.7, and with no consistent difference in the quality of the predictions from the various methods. For one set of ligands, the results could be strongly improved (after experimental data were revealed) if it was recognised that one of the ligands displaced one or two water molecules. For the other two sets, the problem is probably that the ligands bind in different modes than in the crystal structures employed or that the conformation of the ligand-binding site or the whole protein changes.
Electronic supplementary material
The online version of this article (doi:10.1007/s10822-016-9942-z) contains supplementary material, which is available to authorized users.
doi:10.1007/s10822-016-9942-z
PMCID: PMC5078160  PMID: 27565797
Ligand-binding affinity; Induced-fit docking; MM/GBSA; QM/MM; Big-QM; Free-energy perturbation; Continuum solvation; Bennett acceptance ratio; D3R grand challenge; Blind-test competition
20.  Structural, Spectroscopic, and Computational Characterization of the Azide Adduct of FeIII(2,6-diacetylpyridinebis(semioxamazide)), a Functional Analogue of Iron Superoxide Dismutase 
Inorganic chemistry  2013;52(15):8909-8918.
We have prepared and thoroughly characterized, using X-ray crystallographic, spectroscopic, and computational methods, the diazide adduct of [FeIII(dapsox)(H2O)2]1+ [dapsox=2,6-diacetylpyridinebis(semioxamazide)] (1), alow-molecular weight, functional analogue of iron superoxide dismutase (FeSOD). The X-ray crystal structure of the dimeric form of 1, (Na[FeIII(dapsox)(N3)2] DMF)2 (2) shows two axially coordinated, symmetry inequivalent azides with differing Fe–N3 bond lengths and Fe–N–N2 bond angles. This inequivalence of the azide ligands likely reflects the presence of an inter-dimer H-bonding interaction between a dapsox NH group and the coordinated nitrogen of one of the two azide ligands. Resonance Raman (rR) data obtained for frozen aqueous solution and solid-state samples of 2 indicate that the azides remain inequivalent in solution, suggesting that one of the azide ligands of 1 engages in an intermolecular hydrogen bonding interaction with a water molecule. Density functional theory (DFT) and time-dependent DFT calculations have been used to study two different computational models of 1, one using coordinates taken from the X-ray crystal structure of 2, and the other generated via DFT geometry optimization. An evaluation of these models on the basis of electronic absorption, magnetic circular dichroism, and rR data indicates that the crystal structure based model provides a more accurate electronic structure description of 1, providing further support for the proposed intermolecular hydrogen bonding of 1 in the solid state and in solution. An analysis of the experimentally validated DFT results for this model reveals that the azides have both σ- and π-bonding interactions with the FeIII center and that more negative charge is located on the Fe-bound, rather than on the terminal, nitrogen atom of each azide. These observations are reminiscent of the results previously reported for the azide adduct of FeSOD and provide clues regarding the origin the high catalytic activity of Fe-dapsox for superoxide disproportionation.
doi:10.1021/ic401098x
PMCID: PMC3974274  PMID: 23875582
21.  Crystal structure of di­chlorido­(2,2′:6′,2′′-terpyridine-κ3 N,N′,N′′)zinc: a redeter­min­ation 
The crystal structure of the title compound, [ZnCl2(C15H11N3)], was redetermined based on modern CCD data. In comparison with the previous determination from photographic film data [Corbridge & Cox (1956 ▶). J. Chem. Soc. 159, 594–603; Einstein & Penfold (1966 ▶). Acta Cryst. 20, 924–926], all non-H atoms were refined with anisotropic displacement parameters, leading to a much higher precision in terms of bond lengths and angles [e.g. Zn—Cl = 2.2684 (8) and 2.2883 (11) compared to 2.25 (1) and 2.27 (1) Å]. In the title mol­ecule, the ZnII atom is five-coordinated in a distorted square-pyramidal mode by two Cl atoms and by the three N atoms from the 2,2′:6′,2′′-terpyridine ligand. The latter is not planar and shows dihedral angles between the least-squares planes of the central pyridine ring and the terminal rings of 3.18 (8) and 6.36 (9)°. The mol­ecules in the crystal structure pack with π–π inter­actions [centroid–centroid distance = 3.655 (2) Å] between pyridine rings of neighbouring terpyridine moieties. These, together with inter­molecular C—H⋯Cl inter­actions, stablize the three-dimensional structure.
doi:10.1107/S1600536814023605
PMCID: PMC4257341  PMID: 25484786
crystal structure; redetermination; 2,2′:6′,2′′-terpyridine; zinc complex; π–π inter­actions
22.  Crystal structure of an unknown solvate of (piperazine-κN){5,10,15,20-tetra­kis­[4-(benzo­yloxy)phen­yl]porphyrinato-κ4 N}zinc 
The mol­ecular structure of the piperazine[5,10,15,20-(tetra­phenyl­benzoate)porphyrinato-κ4 N]zinc(II) complex is composed of parallel pairs of layers with an inter­layer distance of 4.100 Å while the distance between two pairs of layers is 4.047 Å.
The title compound, [Zn(C72H44N4O8)(C4H10N2)] or [Zn(TPBP)(pipz] (where TPBP and pipz are 5,10,15,20-tetra­kis­[4-(benzo­yloxy)phen­yl]porphyrinato and piperazine ligands respectively), features a distorted square-pyramidal coordin­ation geometry about the central ZnII atom. This central atom is chelated by the four N atoms of the porphyrinate anion and further coordinated by a nitro­gen atom of the piperazine axial ligand, which adopts a chair confirmation. The average Zn—N(pyrrole) bond length is 2.078 (7) Å and the Zn— N(pipz) bond length is 2.1274 (19) Å. The zinc cation is displaced by 0.4365 (4) Å from the N4C20 mean plane of the porphyrinate anion toward the piperazine axial ligand. This porphyrinate macrocycle exhibits major saddle and moderate ruffling deformations. In the crystal, the supra­molecular structure is made by parallel pairs of layers along (100), with an inter­layer distance of 4.100 Å while the distance between two pairs of layers is 4.047 Å. A region of electron density was treated with the SQUEEZE [Spek (2015 ▸). Acta Cryst. C71, 9–18] procedure in PLATON following unsuccessful attempts to model it as being part of disordered n-hexane solvent and water mol­ecules. The given chemical formula and other crystal data do not take into account these solvent mol­ecules.
doi:10.1107/S2056989016009269
PMCID: PMC4992910  PMID: 27555935
crystal structure; zinc porphyrin; piperazine; hydrogen bonds; UV–visible spectra
23.  An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics 
An empirically parameterized intermolecular force field is developed for crystal structure modelling and prediction. The model is optimized for use with an atomic multipole description of electrostatic interactions.
We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%.
doi:10.1107/S2052520616007708
PMCID: PMC4971546  PMID: 27484370
lattice energy; crystal structure prediction; multipoles; polarization; electrostatics
24.  Origin and structure of polar domains in doped molecular crystals 
Nature Communications  2016;7:13351.
Doping is a primary tool for the modification of the properties of materials. Occlusion of guest molecules in crystals generally reduces their symmetry by the creation of polar domains, which engender polarization and pyroelectricity in the doped crystals. Here we describe a molecular-level determination of the structure of such polar domains, as created by low dopant concentrations (<0.5%). The approach comprises crystal engineering and pyroelectric measurements, together with dispersion-corrected density functional theory and classical molecular dynamics calculations of the doped crystals, using neutron diffraction data of the host at different temperatures. This approach is illustrated using centrosymmetric α-glycine crystals doped with minute amounts of different L-amino acids. The experimentally determined pyroelectric coefficients are explained by the structure and polarization calculations, thus providing strong support for the local and global understanding of how different dopants influence the properties of molecular crystals.
Doping can introduce structural distortions in a molecular crystal in the form of polar domains. Here, the authors combine pyroelectric measurements and computation to reveal the molecular structure of such domains in centrosymmetric α-glycine crystals doped with L-amino acids.
doi:10.1038/ncomms13351
PMCID: PMC5105173  PMID: 27824050
25.  Complex Stoichiometry-Dependent Reordering of 3,4,9,10-Perylenetetracarboxylic Dianhydride on Ag(111) upon K Intercalation 
ACS Nano  2015;10(2):2365-2374.
Alkali metal atoms are frequently used for simple yet efficient n-type doping of organic semiconductors and as an ingredient of the recently discovered polycyclic aromatic hydrocarbon superconductors. However, the incorporation of dopants from the gas phase into molecular crystal structures needs to be controlled and well understood in order to optimize the electronic properties (charge carrier density and mobility) of the target material. Here, we report that potassium intercalation into the pristine 3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA) monolayer domains on a Ag(111) substrate induces distinct stoichiometry-dependent structural reordering processes, resulting in highly ordered and large KxPTCDA domains. The emerging structures are analyzed by low-temperature scanning tunneling microscopy, scanning tunneling hydrogen microscopy (ST[H]M), and low-energy electron diffraction as a function of the stoichiometry. The analysis of the measurements is corroborated by density functional theory calculations. These turn out to be essential for a correct interpretation of the experimental ST[H]M data. The epitaxy types for all intercalated stages are determined as point-on-line. The K atoms adsorb in the vicinity of the oxygen atoms of the PTCDA molecules, and their positions are determined with sub-Ångström precision. This is a crucial prerequisite for the prospective assessment of the electronic properties of such composite films, as they depend rather sensitively on the mutual alignment between donor atoms and acceptor molecules. Our results demonstrate that only the combination of experimental and theoretical approaches allows for an unambiguous explanation of the pronounced reordering of KxPTCDA/Ag(111) upon changing the K content.
doi:10.1021/acsnano.5b07145
PMCID: PMC4768340  PMID: 26718635
potassium intercalation; self-assembled nanostructures; low-temperature scanning tunneling microscopy (LT-STM); scanning tunneling hydrogen microscopy (STHM); density functional theory (DFT); low-energy electron diffraction (LEED)

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