Does the choice of the crystal structure influence the results of the periodic DFT calculations? A case of glycine alpha polymorph GIPAW NMR parameters computations

Glycine is a common amino acid with relatively complex chemistry in solid state. Although several polymorphs (α, β, δ, γ, ε) of crystalline glycine are known, for NMR spectroscopy the most important is a polymorph, which is used as a standard for calibration of spectrometer performance and therefore it is intensively studied by both experimental methods and theoretical computation. The great scientific interest in a glycine results in a large number of crystallographic information files (CIFs) deposited in Cambridge Structural Database (CSD). The aim of this study was to evaluate the influence of the chosen crystal structure of α glycine obtained in different crystallographic experimental conditions (temperature, pressure and source of radiation of α glycine) on the results of periodic DFT calculation. For this purpose the total of 136 GIPAW calculations of α glycine NMR parameters were performed, preceded by the four approaches (“SP”, “only H”, “full”, “full+cell”) of structure preparation. The analysis of the results of those computations performed on the representative group of 34 structures obtained at various experimental conditions revealed that though the structures were generally characterized by good accuracy (R < 0.05 for most of them) the results of the periodic DFT calculations performed using the unoptimized structures differed significantly. The values of the standard deviations of the studied NMR parameters were in most cases decreasing with the number of optimized parameters. The most accurate results (of the calculations) were in most cases obtained using the structures with solely hydrogen atoms positions optimized. © 2018 Wiley Periodicals, Inc.     

Quantitative Structural Constraints for Organic Powders at Natural Isotopic Abundance Using Dynamic Nuclear Polarization Solid‐State NMR Spectroscopy

A straightforward method is reported to quantitatively relate structural constraints based on ¹³C–¹³C double‐quantum build‐up curves obtained by dynamic nuclear polarization (DNP) solid‐state NMR to the crystal structure of organic powders at natural isotopic abundance. This method relies on the significant gain in NMR sensitivity provided by DNP (approximately 50‐fold, lowering the experimental time from a few years to a few days), and is sensitive to the molecular conformation and crystal packing of the studied powder sample (in this case theophylline). This method allows trial crystal structures to be rapidly and effectively discriminated, and paves the way to three‐dimensional structure elucidation of powders through combination with powder X‐ray diffraction, crystal‐structure prediction, and density functional theory computation of NMR chemical shifts.     

Solid-State NMR-Driven Crystal Structure Prediction of Molecular Crystals: The Case of Mebendazole

Among all possible NMR crystallography approaches for crystal-structure determination, crystal structure prediction – NMR crystallography (CSP-NMRX) has recently turned out to be a powerful method. In the latter, the original procedure exploited solid-state NMR (SSNMR) information during the final steps of the prediction. In particular, it used the comparison of computed and experimental chemical shifts for the selection of the correct crystal packing. Still, the prediction procedure, generally carried out with DFT methods, may require important computational resources and be quite time-consuming, especially if there are no available constraints to use at the initial stage. Herein, the successful application of this combined prediction method, which exploits NMR information also in the input step to reduce the search space of the predictive algorithm, is presented. Herein, this method was applied on mebendazole, which is characterized by desmotropism. The use of SSNMR data as constraints for the selection of the right tautomer and the determination of the number of independent molecules in the unit cell led to a considerably faster process, reducing the number of calculations to be performed. In this way, the crystal packing was successfully predicted for the three known phases of mebendazole. To evaluate the quality of the predicted structures, these were compared to the experimental ones. The crystal structure of phase B of mebendazole, in particular, was determined de novo by powder diffraction and is presented for the first time in this paper.     

Spectroscopic investigation (IR and NMR) and HOMO-LUMO analysis of aromatic imines using theoretical approach

In this work, the theoretical studies on the structure, FT-IR, NMR, and UV–Vis spectroscopy of (E)-N-benzylidenebenzenamine (A1) and (E)-N-(2, 4′-dichlorobenzylidene) propan-1-amine (A2) are presented. The optimized structure of the molecules, NMR and UV–Vis spectra analysis were determined by the Density Functional Theory (DFT) method using B3LYP/6-311G (d, p) basis set. For FT-IR analysis, both the HF and DFT methods were used in order to determine their accuracy and reliability in theoretical calculations. The computed result of DFT calculations in comparison with the experimental results showed that the DFT method gives a more accurate prediction. The infrared (IR) spectra for the imine molecules have been recorded in the region of 500–4000 cm^?1. The gauge-independent atomic orbital (GIAO) method has been used to evaluate the ¹³C and ¹H nuclear magnetic resonance (NMR) chemical shifts of the molecules. The computed results of NMR spectra of the molecules was found to be in good agreement with the experimental data. The UV–Vis spectra of the molecules were computed to determine the HOMO-LUMO energies in order to gain insight into their electronic properties. Mulliken population analysis on atomic charges of the molecules was also calculated using the HF (Hartree-Fock) and B3LYP method. All the computed results indicated that the B3LYP method provides satisfactory results and, therefore, can be employed to support experimental data. It also demonstrated a reliable approach towards characterization of molecules in chemical science.     

The use of variable temperature 13C solid-state MAS NMR and GIPAW DFT calculations to explore the dynamics of diethylcarbamazine citrate

Experimental ¹³C solid-state magic-angle spinning (MAS) Nuclear Magnetic Resonance (NMR) as well as Density-Functional Theory (DFT) gauge-including projector augmented wave (GIPAW) calculations were used to probe disorder and local mobility in diethylcarbamazine citrate, (DEC)⁺(citrate)⁻. This compound has been used as the first option drug for the treatment of filariasis, a disease endemic in tropical countries and caused by adult worms of Wuchereria bancrofti, which is transmitted by mosquitoes. We firstly present 2D ¹³C─¹H dipolar-coupling-mediated heteronuclear correlation spectra recorded at moderate spinning frequency, to explore the intermolecular interaction between DEC and citrate molecules. Secondly, we investigate the dynamic behavior of (DEC)⁺(citrate)⁻ by varying the temperature and correlating the experimental MAS NMR results with DFT GIPAW calculations that consider two (DEC)⁺ conformers (in a 70:30 ratio) for crystal structures determined at 293 and 235 K. Solid-state NMR provides insights on slow exchange dynamics revealing conformational changes involving particularly the DEC ethyl groups.     

Concomitant Polymorphism in an Organic Solid: Molecular and Crystal Structure and Intra- and Intermolecular Potential Contributions to tert-Butyl and Methyl Group Rotation

We investigate the relationship between structure (crystal and molecular) and tert-butyl and methyl group dynamics in 2-(tert-butyl)-9-(4-(tert-butyl)phenyl)anthracene. Powder and single-crystal X-ray diffraction, taken together, show that different polycrystalline samples recrystallized from different solvents have different amounts of at least four polymorphs (crystallites having different crystal structures), of which we have identified three by single crystal X-ray diffraction. The molecules in the asymmetric units of the different crystal structures differ by the dihedral angle the tert-butylphenyl group makes with the anthracene moiety. Ab initio electronic structure calculations on the isolated molecule show that very little intramolecular energy is required to change this angle over a range of about 60° which is probably the origin of the concomitant polymorphism (crystals of more than one polymorph in a polycrystalline sample). Solid state ¹H nuclear magnetic resonance (NMR) spin-lattice relaxation experiments support the powder and single-crystal X-ray results and provide average NMR activation energies (closely related to rotational barriers) for the rotation of the tert-butyl groups and their constituent methyl groups. These barriers have both an intramolecular and an intermolecular component. The latter is sensitive to the crystal structure. The intramolecular components of the rotational barriers of the two tert-butyl groups in the isolated molecule are investigated with ab initio electronic structure calculations.     

1H NMR analysis of O‐methyl‐inositol isomers: a joint experimental and theoretical study

Density functional theory (DFT) calculations of ¹H NMR chemical shifts for l ‐quebrachitol isomers were performed using the B3LYP functional employing the 6‐31G(d,p) and 6‐311 + G(2d,p) basis sets. The effect of the solvent on the B3LYP‐calculated NMR spectrum was accounted for using the polarizable continuum model. Comparison is made with experimental ¹H NMR spectroscopic data, which shed light on the average uncertainty present in DFT calculations of chemical shifts and showed that the best match between experimental and theoretical B3LYP ¹H NMR profiles is a good strategy to assign the molecular structure present in the sample handled in the experimental measurements. Among four plausible O‐methyl‐inositol isomers, the l ‐quebrachitol 2a structure was unambiguously assigned based only on the comparative analysis of experimental and theoretical ¹H NMR chemical shift data. The B3LYP infrared (IR) spectrum was also calculated for the four isomers and compared with the experimental data, with analysis of the theoretical IR profiles corroborating assignment of the 2a structure. Therefore, it is confirmed in this study that a combined experimental/DFT spectroscopic investigation is a powerful tool in structural/conformational analysis studies. Copyright © 2012 John Wiley & Sons, Ltd.     

Investigation of structure and dynamics in a photochromic molecular crystal by NMR crystallography

A photochromic anil, N-(3,5-di-t-butylsalicylidene)-4-amino-pyridine, has been studied by single-crystal X-ray diffraction, multinuclear magic-angle spinning NMR, and first-principles density functional theory (DFT) calculations. Interpretation of the solid-state NMR data on the basis of calculated chemical shifts confirms the structure is primarily composed of molecules in the ground-state enol tautomer, whereas thermally activated cis-keto and photoisomerised trans-keto states exist as low-level defects with populations that are too low to detect experimentally. Variable temperature ¹³C NMR data reveal evidence for solid-state dynamics, which is found to be associated with fast rotational motion of t-butyl groups and 180° flips of the pyridine ring, contrasting the time-averaged structure obtained by X-ray diffraction. Comparison of calculated chemical shifts for the full crystal structure and an isolated molecule also reveals evidence for an intermolecular hydrogen bond involving the pyridine ring and an adjacent imine carbon, which facilitates the flipping motion. The DFT calculations also reveal that the molecular conformation in the crystal structure is very close to the energetic minimum for an isolated molecule, indicating that the ring dynamics arise as a result of considerable steric freedom of the pyridine ring and which also allows the molecule to adopt a favourable conformation for photochromism.     

Ab initio and semiempirical computational studies on 1‐{(2E)‐2‐[(aminocarbonothioyl)hydrazono]‐2‐(3‐mesityl‐3‐methylcyclobutyl)ethyl}‐pyrrolidine‐2,5‐dione

The molecular geometry, vibrational frequencies, and gauge including atomic orbital (GIAO) ¹H‐ and ¹³C NMR chemical shift values of the title compound in the ground state have been calculated using the Hartree‐Fock (HF) and density functional theory (DFT) methods with 6‐31G(d) basis sets, and compared with the experimental data. The calculated results show that the optimized geometries can well reproduce the crystal structural parameters and the theoretical vibrational frequencies, and ¹H‐ and ¹³C NMR chemical shift values show good agreement with experimental data. To determine conformational flexibility, the molecular energy profile of the title compound was obtained by semiempirical (AM1) calculations with respect to the selected torsion angle, which was varied from ?180° to +180° in steps of 10°. The energetic behavior of the title compound in solvent media was examined using the B3LYP method with the 6‐31G(d) basis set by applying the Onsager and the polarizable continuum model (PCM). The results obtained with these methods reveal that the PCM method provided more stable structure than Qnsager's method. By using TD‐DFT method, electronic absorption spectra of the title compound have been predicted and a good agreement with the TD‐DFT method and the experimental one is determined. The predicted nonlinear optical properties of the title compound are much greater than ones of urea. In addition, the molecular electrostatic potential (MEP), frontier molecular orbitals (FMO) analysis, NBO analysis and thermodynamic properties of the title compound were investigated using theoretical calculations. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

An NMR crystallography investigation of furosemide

This paper presents an NMR crystallography study of three polymorphs of furosemide. Experimental magic-angle spinning (MAS) solid-state NMR spectra are reported for form I of furosemide, and these are assigned using density-functional theory (DFT)-based gauge-including projector augmented wave (GIPAW) calculations. Focusing on the three known polymorphs, we examine the changes to the NMR parameters due to crystal packing effects. We use a recently developed formalism to visualise which regions are responsible for the chemical shielding of particular sites and hence understand the variation in NMR parameters between the three polymorphs.     

Solid-State Nuclear Magnetic Resonance Techniques for the Structural Characterization of Geminal Alane-Phosphane Frustrated Lewis Pairs and Secondary Adducts

The first comprehensive solid-state nuclear magnetic resonance (NMR) characterization of geminal alane-phosphane frustrated Lewis pairs (Al/P FLPs) is reported. Their relevant NMR parameters (isotropic chemical shifts, direct and indirect ²⁷Al-³¹P spin-spin coupling constants, and ²⁷Al nuclear electric quadrupole coupling tensor components) have been determined by numerical analysis of the experimental NMR line shapes and compared with values computed from the known crystal structures by using density functional theory (DFT) methods. Our work demonstrates that the ³¹P NMR chemical shifts for the studied Al/P FLPs are very sensitive to slight structural inequivalences. The ²⁷Al NMR central transition signals are spread out over a broad frequency range (>200 kHz), owing to the presence of strong nuclear electric quadrupolar interactions that can be well-reproduced by the static ²⁷Al wideband uniform rate smooth truncation (WURST) Carr-Purcell-Meiboom-Gill (WCPMG) NMR experiment. ²⁷Al chemical shifts and quadrupole tensor components offer a facile and clear distinction between three- and four-coordinate aluminum environments. For measuring internuclear Al⋅⋅⋅P distances a new resonance-echo saturation-pulse double-resonance (RESPDOR) experiment was developed by using efficient saturation via frequency-swept WURST pulses. The successful implementation of this widely applicable technique indicates that internuclear Al⋅⋅⋅P distances in these compounds can be measured within a precision of ±0.1 Å.     

A Combined Solid‐State NMR and X‐ray Crystallography Study of the Bromide Ion Environments in Triphenylphosphonium Bromides

Multinuclear (³¹P and ^79/81Br), multifield (9.4, 11.75, and 21.1 T) solid‐state nuclear magnetic resonance experiments are performed for seven phosphonium bromides bearing the triphenylphosphonium cation, a molecular scaffold found in many applications in chemistry. This is undertaken to fully characterise their bromine electric field gradient (EFG) tensors, as well as the chemical shift (CS) tensors of both the halogen and the phosphorus nuclei, providing a rare and novel insight into the local electronic environments surrounding them. New crystal structures, obtained from single‐crystal X‐ray diffraction, are reported for six compounds to aid in the interpretation of the NMR data. Among them is a new structure of BrPPh₄, because the previously reported one was inconsistent with our magnetic resonance data, thereby demonstrating how NMR data of non‐standard nuclei can correct or improve X‐ray diffraction data. Our results indicate that, despite sizable quadrupolar interactions, ^79/81Br magnetic resonance spectroscopy is a powerful characterisation tool that allows for the differentiation between chemically similar bromine sites, as shown through the range in the characteristic NMR parameters. ^35/37Cl solid‐state NMR data, obtained for an analogous phosphonium chloride sample, provide insight into the relationship between unit cell volume, nuclear quadrupolar coupling constants, and Sternheimer antishielding factors. The experimental findings are complemented by gauge‐including projector‐augmented wave (GIPAW) DFT calculations, which substantiate our experimentally determined strong dependence of the largest component of the bromine CS tensor, δ₁₁, on the shortest Br? P distance in the crystal structure, a finding that has possible application in the field of NMR crystallography. This trend is explained in terms of Ramsey’s theory on paramagnetic shielding. Overall, this work demonstrates how careful NMR studies of underexploited exotic nuclides, such as ^79/81Br, can afford insights into structure and bonding environments in the solid state.     

Effect of Electronic Structures of Enantiomers of Ruthenium(II) Polypyridyl Complexes on DNA Binding Behaviors

A pair of Ru(II) complex enantiomers, Δ‐ and Λ‐[Ru(bpy)₂(p‐mpip)]²⁺ {bpy=2,2′‐bipyridine, p‐mpip=2‐(4‐methylphenyl)imidazo[4,5‐f]‐1,10‐phenanthroline} have been synthesized and structurally characterized. Both experimental results from crystallography, NMR, electrochemistry and theoretical calculations applying the density functional theory (DFT) method based on their crystal structures show that small difference in geometric structure existed can cause a considerable difference in electronic structure between enantiomers. In addition, the binding of the two enantiomers to calf thymus DNA (CT DNA) has been investigated with UV spectroscopy titration and viscosity measurements. It is very rare that the Λ enantiomer binds to DNA more strongly than the Δ enantiomer, which can be reasonably explained by their different electronic structures for the first time, suggesting that the dominant factor governing the stereoselectivity of DNA binding of Ru(II) complex may be the different electronic structures of its enantiomers.     

1,3-二甲基-2-二茂铁甲基苯并咪唑碘盐的合成、表征、晶体结构及量子化学计算

A novel benzimidazole derivative, 1,3-dimethyl-2-ferrocenylmethylbenzimidazolium iodide （1） was synthesized and characterized by elemental analysis, MS, IH NMR and IR spectra. Its crystal structure was determined by X-ray single crystal diffraction, and the title compound belongs to monoclinic system with space group P2（1）/c. According to the crystal structure, the quantum chemistry calculation was performed by Gaussian 03 program, and full geometry optimizations of the title compound were carried out with DFT method at B3LYP/6-31G level. Its structure, stability, frontier molecular orbital components and net charge distribution were discussed.     

Quantum‐chemical,IR, NMR,and X‐ray diffraction studies on 2‐(4‐chlorophenyl)‐1‐methyl‐ 1H‐benzo[d]imidazole

The title molecule, 2‐(4‐chlorophenyl)‐1‐methyl‐1H‐benzo[d]imidazole (C₁₄H₁₁ClN₂), was prepared and characterized by ¹H NMR, ¹³C NMR, IR, and single‐crystal X‐ray diffraction. The molecular geometry, vibrational frequencies, and gauge including atomic orbital (GIAO) ¹H and ¹³C NMR chemical shift values of the title compound in the ground state have been calculated by using the Hartree‐Fock (HF) and density functional theory (DFT/B3LYP) method with 6‐31G(d) basis sets, and compared with the experimental data. The calculated results show that the optimized geometries can well reproduce the crystal structural parameters, and the theoretical vibrational frequencies and GIAO ¹H and ¹³C NMR chemical shifts show good agreement with experimental values. The energetic behavior of the title compound in solvent media has been examined using B3LYP method with the 6‐31G(d) basis set by applying the Onsager and the polarizable continuum model (PCM). Besides, molecular electrostatic potential (MEP), frontier molecular orbitals (FMO) analysis, and nonlinear optical (NLO) properties of the title compound were investigated by theoretical calculations. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

DFT-calculated structures based on 1H NMR chemical shifts in solution vs. structures solved by single-crystal X-ray and crystalline-sponge methods: Assessing specific sources of discrepancies

DFT calculations of ¹H NMR chemical shifts, using various functionals and basis sets, the conductor-like polarizable continuum model and discrete solute-solvent hydrogen bond interactions have been used to derive the solution structures of methyl salicylate and methyl 2,5-dihydroxybenzoate. We demonstrate that very good agreement between experimental and computed ¹H NMR chemical shifts can be obtained for various basis sets. The DFT structures in solution were compared with the recently reported X-ray structure, solved by the crystalline-sponge method, of the methyl salicylate and the single-crystal X-ray structure of methyl 2,5-dihydroxybenzoate. It is demonstrated that the information provided by ¹H NMR chemical shifts about the solution structure is significantly more precise than that obtained by the single-crystal X-ray and the crystalline-sponge methods.     

Multinuclear Solid‐State Magnetic Resonance as a Sensitive Probe of Structural Changes upon the Occurrence of Halogen Bonding in Co‐crystals

Although the understanding of intermolecular interactions, such as hydrogen bonding, is relatively well‐developed, many additional weak interactions work both in tandem and competitively to stabilize a given crystal structure. Due to a wide array of potential applications, a substantial effort has been invested in understanding the halogen bond. Here, we explore the utility of multinuclear (¹³C, ^14/15N, ¹⁹F, and ¹²⁷I) solid‐state magnetic resonance experiments in characterizing the electronic and structural changes which take place upon the formation of five halogen‐bonded co‐crystalline product materials. Single‐crystal X‐ray diffraction (XRD) structures of three novel co‐crystals which exhibit a 1:1 stoichiometry between decamethonium diiodide (i.e., [(CH₃)₃N⁺(CH₂)₁₀N⁺(CH₃)₃][2 I^?]) and different para‐dihalogen‐substituted benzene moieties (i.e., p‐C₆X₂Y₄, X=Br, I; Y=H, F) are presented. ¹³C and ¹⁵N NMR experiments carried out on these and related systems validate sample purity, but also serve as indirect probes of the formation of a halogen bond in the co‐crystal complexes in the solid state. Long‐range changes in the electronic environment, which manifest through changes in the electric field gradient (EFG) tensor, are quantitatively measured using ¹⁴N NMR spectroscopy, with a systematic decrease in the ¹⁴N quadrupolar coupling constant (C_Q) observed upon halogen bond formation. Attempts at ¹²⁷I solid‐state NMR spectroscopy experiments are presented and variable‐temperature ¹⁹F NMR experiments are used to distinguish between dynamic and static disorder in selected product materials, which could not be conclusively established using solely XRD. Quantum chemical calculations using the gauge‐including projector augmented‐wave (GIPAW) or relativistic zeroth‐order regular approximation (ZORA) density functional theory (DFT) approaches complement the experimental NMR measurements and provide theoretical corroboration for the changes in NMR parameters observed upon the formation of a halogen bond.     

Undeniable Confirmation of the syn‐Addition Mechanism for Metal‐Free Diboration by Using the Crystalline Sponge Method

The stereochemical outcome of the recently developed metal‐free 1,2‐diboration of aliphatic alkenes has, until now, only been elucidated by indirect means (e.g. derivatization). This is because classical conformational analysis of the resulting 1,2‐diboranes is not viable; in the ¹H NMR spectrum the relevant ¹H resonances are broadened by ¹¹B, and the occurrence of the products as oily compounds precludes X‐ray crystallographic analysis. Herein, the crystalline sponge method is used to display the crystal structures of the diboronic esters formed from internal E and Z olefins, evidencing the stereospecific syn addition mechanism of the reaction, which is fully consistent with the prediction from DFT calculations.     

Molecular Structure and a Density Functional Theoretical Study on 2‐Nitroimino‐5‐Nitro‐Hexahydro‐1,3,5‐Triazine (NNHT)

2‐Nitroimino‐5‐nitro‐hexahydro‐1,3,5‐triazine (NNHT), was synthesized and its structure was determined by single‐crystal X‐ray diffraction. The crystal is monoclinic, space group P2₁/c with crystal parameters of a = 9.4031(13) Å, b = 8.5891(12) Å, c = 9.0200(13) Å, β = 91.213(2)°, V = 728.33(18) ų, Z = 4, F(000) = 392, D_c = 1.734 g/cm³. The experimental geometry of NNHT was input to Gaussian‐03W program and optimized using DFT‐B3LYP/6‐311++G** method. The IR frequencies and NMR chemical shift were carried out and compared well with those of the experimental. The atomic net charges and the population analysis are discussed. The heat of formation (HOF) for NNHT was evaluated by designing an isodesmic reaction. The detonation velocity (D) and detonation pressure (P) were estimated by using the well known Kamlet‐Jacobs equation, based on the theoretical HOF.