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Elucidation of the Interaction Mechanism between Organic Chiral Cages with Biomolecules through Nuclear Magnetic Resonance and Theoretical Studies
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  • Sara Sáez-Ferre
    Sara Sáez-Ferre
    Instituto de Tecnología Química, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas (UPV-CSIC), Avda. de los Naranjos s/n, 46022 Valencia, Spain
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  • Mercedes Boronat
    Mercedes Boronat
    Instituto de Tecnología Química, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas (UPV-CSIC), Avda. de los Naranjos s/n, 46022 Valencia, Spain
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  • Ángel Cantín
    Ángel Cantín
    Instituto de Tecnología Química, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas (UPV-CSIC), Avda. de los Naranjos s/n, 46022 Valencia, Spain
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  • Fernando Rey*
    Fernando Rey
    Instituto de Tecnología Química, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas (UPV-CSIC), Avda. de los Naranjos s/n, 46022 Valencia, Spain
    *E-mail: [email protected] (F.R.).
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    Orcidhttp://orcid.org/0000-0003-3227-5669
  • Pascual Oña-Burgos*
    Pascual Oña-Burgos
    Instituto de Tecnología Química, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas (UPV-CSIC), Avda. de los Naranjos s/n, 46022 Valencia, Spain
    *E-mail: [email protected] (P.O.-B.).
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    Orcidhttp://orcid.org/0000-0002-2341-7867
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The Journal of Physical Chemistry C

Cite this: J. Phys. Chem. C 2018, 122, 29, 16821–16829
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https://doi.org/10.1021/acs.jpcc.8b05069
Published July 2, 2018

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Abstract

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A multinuclear NMR has been carried out to elucidate the mechanism of action of CC3-R box-type chiral materials for the separation of enantiomers, supported by theoretical calculations. The potential of these materials to be used as chiral resolution agents through NMR is evidence in this study.

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Introduction

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Enantiomers have physical and chemical identical properties except for optical rotation; and they also have different biological and pharmacological properties. Therefore, chiral discrimination has become more important in several fields, as in the pharmaceutical industry, in stereospecific synthesis, in the food industry, environmental science, and development of optical devices. (1,2) However, the separation of enantiomers is still a challenge because of their physical and chemical identical properties.
Microporous small pore size crystalline materials have been of great scientific and technological interest because of their potential applications in gas storage, heterogeneous catalysis, and molecular separation. Most microporous solids are formed by extended three-directional networks such as, zeolites, (3−5) metal–organic frameworks, (6−11) covalent–organic frameworks (COFs), (12−14) or organic polymer networks. (15,16)
Contrary to extended networks, porous organic molecular solids (POMs) can be soluble in organic solvents. The solubility of POMs offers some advantages in comparison to insoluble networks materials. Their monomers retain the same structural porosity as the original POMs after dissolution in common organic solvents and are easily recrystallized. These POMs seem to open new avenues for promising further applications.
On this regard, the Cooper research’s group synthesized a new class of porous organic cages (POCs) with permanent and available cavities formed via condensation reaction of 1,3,5-triformylbenzene or tris(4-formylphenyl)amine and various diamines and evidenced the cage–cage self-assemble into crystalline materials with permanent void space. (17−24) Cooper and co-workers first reported the synthesis of POC (CC3) and its use for chiral separation. (19,23)
CC3 is an imine-linked POC, which is synthesized by the one-step [4 + 6] condensation of 1,3,5-triformylbenzene with (R,R)-1,2-diaminocyclohexane or (S,S)-1,2-diaminocyclohexane. This cage has tetrahedral symmetry, and each cage has four windows, the cage molecules pack in a window-to-window arrangement that self-assemble into perfectly ordered materials. Porous organic molecular cages defined as shape-persistent three-dimensional organic molecules have been explored for gas adsorption, separation, molecular recognition, and sensing. More recently, CC3-R has been used in gas-chromatographic (GC) separation. Particularly, CC3-R has been successfully used in the enantiomeric resolution of a wide variety of racemates belonging to different classes without derivatization. (25,26)
However, these relevant results are based on trial and error experiments and so far for being trivial, in which racemates can be successfully resolved by a given chiral solid. Therefore, the development of physico-chemical techniques that can be used as screening for the mentioned separations could be of interest for many researchers working in pharmacy, separation, NMR, modeling, and so forth. For instance, there is little insight into the detailed interaction between the host CC3-R entity and the guest molecule. To the best of our knowledge, there is just one report applying to a chiral molecule (1-phenyl-1-ethanol), where racemic mixture of 1-phenyl-1-ethanol is eluted through the chiral material and 30% ee of the opposite configuration is obtained in the solution.
Within this study, we provide information related to the interaction of the material CC3-R with several small chiral organic molecules, many of them biomolecules. Furthermore, we determined the preference of this material to some functional group, and then we have found the application to separate racemic mixture of amino acids (aa) and alpha hydroxyl-acids (ha). In addition, we suggest that these materials are also likely to be used as resolution agents of enantiomers.

Experimental Section

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General Considerations

CC3-R and CC3-S were prepared according to literature procedures (or modified procedures) using solvothermal strategy. (21) The employed guests were purchased from Sigma-Aldrich and used without further purification. The samples for liquid NMR analysis were prepared as follows. CC3-R is dissolved in CD2Cl2 at 2.5 mM. Then, the guest was added to this solution to achieve a final concentration of 1, 3, and 10 mM for each sample.

Solution NMR Spectroscopy

Solution NMR spectra were recorded with Bruker AVANCE instruments operating at 1H Larmor frequency of 300 MHz. Chemical shifts are given in ppm and relative to tetramethylsilane for 1H and 13C and relative to NH3 (liquid) for 15N nuclei. Coupling constants (J) are given in hertz as positive values, regardless of their real individual signs. Pulsed gradient spin-echo (PGSE) NMR diffusion measurements were carried out by using the stimulated echo pulse sequence. (27) A rectangular shape was used for the gradient pulses, and their strengths changed automatically during the course of the experiments. The D values were determined from the slope of the regression line ln(I/I0) versus G2, according to eq 1. I/I0 = observed spin echo intensity/intensity without gradients, G = gradient strength, Δ = delay between the midpoints of the gradients, D = diffusion coefficient, and δ = gradient length. The measurements were performed without spinning. The calibration of the gradients was carried out by means of a diffusion measurement of HDO in D2O (DHDO = 1.902 109 m2 s–1). (28) The experimental error in D values was estimated to be smaller than ±2% (three standard deviations). All of the data that led to the reported D values afforded lines with correlation coefficients above 0.999. The gradient strength was incremented in 8% steps from 10 to 98%, so that, depending on the signal/noise ratio, 10–12 points could be used for regression analysis. Afterward, the Einstein–Stokes formula (eq 2) correlates D with the hydrodynamic radius rH.
(1)
Einstein–Stokes formula
(2)

X-ray Diffraction

The crystallinity of the materials was investigated by powder X-ray diffraction. The measurements were performed using a PANalytical X’Pert PRO diffractometer in a Bragg–Brentano geometry and Cu Kα1 radiation (λ = 1.5406 Å).

Other Techniques

The morphology of the cages was analyzed by scanning electron microscopy (SEM). SEM micrographs were recorded on a SU8230 field emission SEM instrument working at 5–10 kV, using beam deceleration mode. The samples were prepared by placing a small amount of powder on a carbon tape on SEM stubs. C, N, and H contents of isolated catalysts were determined with a Carlo Erba 1106 elemental analyzer. Thermogravimetric analysis (TGA) was carried out using a Mettler Toledo TGA/SDTA851e with an automated vertical overhead thermobalance.

Density Functional Theory Studies

All calculations in this work are based on density functional theory (DFT) and were carried out using the M062X functional (29) and the 6-311g(d,p) basis set, (30) as implemented in the Gaussian 09 software. (31) The geometry of all structures was fully optimized without restrictions. Host–guest interaction energies were calculated as
where E(host–guest) is the total energy of the complexes shown in Figures 5 and S83, and E(host) and E(guest) are the total energies of the isolated host model and guest molecules, respectively.

Results

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The CC3-R material was synthesized using solvothermal conditions. First of all, it was fully characterized by NMR. In fact, diffusion NMR spectroscopy was employed with the aim of measuring diffusion coefficients and estimating hydrodynamic radii of molecules in isotropic media. (32,33) This technique is mostly used to study organometallic complexes, as well as supramolecular systems such as host–guest systems, helicates, grids, supramolecular polymers, and more. Diffusion NMR has also found applications in studies of biosystems, pharmaceutical ones, and those of the structure of nanoparticles. (34−40) It is accepted that the diffusion decrease and the hydrodynamic radius of any species increases as the interaction with the host molecule increase. Therefore, this technique is especially well suited for studying host–guest interactions such as those occurring during adsorption and separation processes.
PGSE NMR diffusion measurements were used to determine the diffusion coefficients (D) of the material CC3-R studied here in solution (more details of these experiments are provided in the Supporting Information). The experiments were performed in CD2Cl2 from 0.25 to 2.5 mM concentrations of material to determine if agglomeration takes place. In Table 1, the diffusion data and hydrodynamic radius for CC3-R are summarized and compared with the radius obtained from X-ray. The results shown in Table 1 indicate that diffusion (D) and hydrodynamic radius of CC3-R remain constant along the whole range of concentration, indicating that there is no agglomeration of the monomers for further experiments.
Table 1. Diffusion Data for CC3-R
entry[CC3-R] [mM]D [10–10 m2 s–1]arH [Å]brX [Å]c
10.25 mM R6.68.18.5
20.75 mM R6.68.1 
32.5 mM R6.68.1 
a

Experimental error in the D values was (±2)%.

b

The viscosity (η) used in the Stokes–Einstein equation was 0.410 × 10–3 kg m–1 s–1. Values of η were taken from http://www.knovel.com.

c

It is an estimation, deduced from the X-ray structure described in the ref (8).

NMR Spectroscopy Study of Host–Guest Interactions

Intrigued by the way of action of materials in exerting the separation of organic molecules and racemates shown above, we propose a full study based on solution NMR that provide a direct and detailed view on the underlying interactions at the molecular level. Solution NMR spectroscopy could provide such a view because intermolecular interactions can be studied through their effect on the chemical shift, relaxation times, and translational diffusion coefficients of the various species. In the case of protein receptors and ligand binding, specific NMR approaches are routinely applied to provide information about the binding process and conformations. Taking advantage of the presence of the permanent porosity of CC3-R material, its high organic content, and its solubility in dichloromethane, we propose NMR-based approaches in host–guest heterogeneous related system for the in situ characterization of the molecular interactions.
First of all, we carried out 1H NMR measurements of the POCs and the different guests at 298 K with concentrations between 1 and 10 mM in CD2Cl2. The solvent chosen is CD2Cl2 because the CC3 materials are fully soluble in this solvent. A number of guests have been employed to carry out this study including, 1-phenyl-ethylamine which Cooper used in his work, other biomolecules derived from protected amino acids in the amino group (Figure 1). For this study, free amino acids were not directly used because of their insolubility in CD2Cl2. Then, the corresponding commercially available BOC-derivated chiral systems in their two enantiomeric forms have been selected, as shown in Figure 1. Then, the measurement of the different samples constituted by the host, CC3-R, and each guest at different concentrations was carried out.

Figure 1

Figure 1. Illustration of the selected guests (L/S red and D/R blue).

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First of all, both the host and the series of guests were studies at 298 K as solution of pure compounds at 10 mM concentration in CD2Cl2. Then, the mixture of each guest (concentrations range from 1 to 10 mM) and the host (concentration of 2.5 mM) was also measured at 298 K in CD2Cl2. In Table 2, the data of these measurements are collected through proton NMR, where the three signals of the COF H1 (imine), H2 (aromatic), and H3 (α-NCH) are analyzed, with the purpose of studying the effect that the presence of different guests used at different concentrations has on the selected 1H NMR resonances of the host CC3-R, which is at a fixed concentration of 2.5 mM (Figure 2).

Figure 2

Figure 2. Illustration of the three selected signals of CC3-R.

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Table 2. 1H NMR Data for the 3 Selected Signals of the Host
  δ 1H NMR [ppm] 
entry[guest] [mM]H1H2H3Δδ H1/H2/H3
1 8.1657.8913.38 
21 mM l-18.1657.8913.3810.000/0.000/0.001
33 mM l-18.1687.9073.3970.003/0.016/0.017
410 mM l-18.1767.9353.4280.011/0.044/0.048
51 mM d-18.1657.8933.3820.000/0.002/0.002
63 mM d-18.1667.9003.3900.001/0.011/0.010
710 mM d-18.1737.9263.4160.008/0.035/0.036
81 mM l-28.1677.8943.3850.002/0.003/0.005
93 mM l-28.1687.8993.3910.003/0.008/0.011
1010 mM l-28.1677.9043.4000.002/0.013/0.020
111 mM d-28.1657.8903.3790.000/0.001/0.001
123 mM d-28.1657.8953.3850.000/0.004/0.005
1310 mM d-28.1657.9023.3960.000/0.011/0.016
141 mM l-38.1657.8903.3790.000/–0.001/0.001
153 mM l-38.1657.8963.3860.000/0.005/0.006
1610 mM l-38.1717.9183.4090.006/0.027/0.029
171 mM d-38.1657.8913.3810.000/0.000/0.001
183 mM d-38.1667.8943.3850.001/0.003/0.005
1910 mM d-38.1687.9103.4000.003/0.019/0.020
201 mM l-48.1677.8943.3840.002/0.003/0.004
213 mM l-48.1677.8973.3890.002/0.006/0.009
2210 mM l-48.1677.8993.3920.002/0.008/0.012
231 mM d-48.1667.8913.3800.001/0.000/0.000
243 mM d-48.1677.8953.3860.002/0.004/0.004
2510 mM d-48.1657.8973.3880.000/0.006/0.008
261 mM l-58.1657.8903.3790.000/–0.001/0.001
273 mM l-58.1657.8913.3800.000/0.000/0.000
2810 mM l-58.1667.8943.3860.001/0.003/0.006
291 mM d-58.1667.8913.3800.001/0.000/0.000
303 mM d-58.1667.8923.3820.001/0.001/0.002
3110 mM d-58.1657.8933.3850.000/0.002/0.005
3210 mM S-68.1627.8893.3780.003/0.003/0.002
3310 mM R-68.1627.8893.3770.003/0.003/0.003
The observed changes in chemical shifts for the three selected COF signals are shown in the right column (guest@COF–COF). There, it is observed that the coupling of lactic acid (compound 1 in Figure 1 with CC3-R material (entries 2–7)) produces a deshielding of the three characteristic resonances of the COF, as evidenced by the displacement toward higher δ of the 1H NMR signal. The deshielding effect is more pronounced as the concentration of lactic acid increases. However more importantly, there is a stronger interaction between the CC3-R and S enantiomers than CC3-R. This phenomenon is clearly illustrated in the Figure 3.

Figure 3

Figure 3. 1H NMR data for H2 signal of the host with both enantiomers of ligand 1 at several concentrations.

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The guests 2 (N-Boc-alanine, inputs 8–13), 3 (N-Boc-valine, inputs 14–19), and 4 (N-Boc-leucine, inputs 20–25) have a similar behavior as described for ligand 1. However, it is less import when the steric effect of the hydrophobic chain is enhanced. In this sense, this effect is slight for guest 5 (N-Boc-proline, inputs 26–31), where only few little changes in the signals of interest are detected for concentrations of 10 mM, and the greatest effect is shown for the L series. Furthermore, as the size of the amino acid aliphatic chain increases, the effect on the host fades. Finally, guest 6 (1-phenylethanol, inputs 32 and 33) has no effect on guest signals in the range of 1–10 mM.
Moreover, if we analyze the data according to the absolute configuration of the host CC3-R used, we can observe how the L series (S absolute configuration) produces a greater effect than the D series (R absolute configuration). However, the shift of 1H NMR signal for experiments of guests 5@CC3-R (entries 26–31) is only observed for the highest guest concentration (10 mM, entries 28 and 31), whilst no significant changes in the NMR signals are observed at lower concentration. Therefore, we can conclude that the CC3-R material has a stronger affinity for carboxylic acid group than the S enantiomer. In addition, this affinity can be nicely modulated by controlling the steric volume of the aliphatic substituent.
A deep study for assessing the binding of guest molecules and the host CC3-R was performed by applying 1H,15N gHMQC and 1H,13C gHSQC NMR experiments. These spectroscopic techniques have been used for understanding the structure–activity relationships (SAR) in biomolecules and proteins. In this sense, NMR spectroscopy is employed to detect binding of drugs to receptor proteins and more important to identify the unit of the protein involved in the process. For instance, 1H,15N gHSQC or HMQC experiments were known to provide an effective method to investigate interactions of the guanidinium groups of arginine units with charged groups on the ligand. (41−47) Another experimental setup to detect binding of ligands to receptor proteins involves the acquisition of 1H,13C gHMQC spectra of probes with and without ligands present. Generally, labeling of proteins with 13C is more expensive than with 15N. Furthermore, 1H,13C gHSQC spectra are more complex than 1H,15N gHSQC spectra. Hence, 1H,13C gHSQC experiments have not been widely employed to test for binding. Nevertheless, in our case, it is not a problem because our host–guest spectra have less signals. Therefore, both experiments were used to demonstrate the interaction between the CC3-R host and the selected molecules. One 1H,15N gHMQC experiment and other of 1H,13C gHSQC of the organic cage CC3-R are acquired as the reference spectra. Then, samples that contain one of the selected molecules (1–6) are prepared. If the resonance position of a cross-peak is significantly shifted compared with the reference spectra, this is an indication of binding (SAR by NMR).
Table 3 shows the carbon-13 NMR data of two signals of the CC3-R C1 (imine), C2 (aromatic), and the nitrogen-15 data for the N1 signal (imine) with the presence of the different guests used at different concentrations, keeping the concentration of the host at 2.5 mM. In addition, in the column on the right, the observed changes in the chemical shifts are shown for the three signals, two of carbon and one of nitrogen, of the host-isolated relative to the corresponding guest–host mix. The close analysis of the data collected in Table 3 indicates that the change in C1 and C2 are very small, suggesting that the interaction between CC3-R and selected guests does not take place through the carbon atoms of the host, and therefore nitrogen atoms must be involved.
Table 3. 13C and 15N NMR Data for the Selected Nuclei of the Host
  δ 13C NMR [ppm]δ 15N NMR [ppm] 
entry[guest] [mM]C1C2N3Δδ C1/C2/N3
1 158.65129.03341.3 
23 mM l-1159.10129.20338.70.45/0.17/2.60
310 mM l-1159.10129.40337.30.45/0.37/4.00
43 mM d-1159.00129.13339.40.35/0.10/1.90
510 mM d-1159.18129.48337.60.53/0.45/3.70
63 mM l-2158.8129.20339.50.15/0.17/1.80
710 mM l-2158.9129.30338.60.25/0.27/2.70
83 mM d-2158.65129.09340.00.00/0.06/1.30
910 mM d-2158.94129.33339.30.29/0.30/2.00
103 mM l-3158.80129.15339.80.15/0.12/1.50
1110 mM l-3159.00129.30338.20.35/0.27/3.10
123 mM d-3158.78129.11340.40.13/0.08/0.90
1310 mM d-3159.80129.13339.10.15/0.10/2.20
143 mM l-4158.94129.13340.90.29/0.10/0.40
2510 mM l-4159.00129.32339.60.34/0.29/1.70
163 mM d-4158.86129.06341.20.21/0.03/0.10
1710 mM d-4158.96129.27340.30.31/0.24/1.00
183 mM l-5158.65129.09341.00.00/0.06/0.30
1910 mM l-5158.80129.20340.40.15/0.17/0.90
203 mM d-5158.74129.03341.60.09/0.00/0.30
2110 mM d-5158.80129.11340.60.15/0.08/0.70
2210 mM S-6158.69129.06341.00.04/0.03/0.30
2310 mM R-6158.67129.04341.10.02/0.01/0.20
Indeed, the changes in the chemical shift of nitrogen are quite significant with the presence of the guests 1–5 indicating that a strong interaction host–guest occurs in good agreement with the observed shifts in 1H NMR signals. Meanwhile, there is practically no effect in the NMR signals when molecule 6 is adsorbed. In addition, the observed changes for 1–4 are in line with what is observed for the proton, where at 3 and 10 mM guest concentrations changes are detected in host signals. Moreover, the effect is higher for L series. However, at guest 5, this is only observed at concentrations of 10 mM, and in all cases slightly higher for the L. This behavior evidences the interactions between both systems through the carboxylic group and the steric effect of the hydrophobic chain decrease this interaction.
After that, it was decided to study the effect that the presence of the host has on guest signals. Table 4 summarizes the proton data between the guest-free and the guest–CC3-R, maintaining the concentration of CC3-R at 2.5 mM and that of the guest at 3 and 10 mM. The associated changes are in line with those observed in the CC3-R. The major changes are those associated with ligand 1 (entries 1–5), and especially the L series, in all cases the signals are shielded. Ligand 2 (entries 6–10) also presents more significant changes for the L than for the D series, this change being of shielding toward the methynic proton and deshielding toward the methyl group. However, for ligands 3–5 (entries 11–23) deshielding happens in all of them, and these deshieldings are greater for the L than for the D series. All these data can be summed up as (1) large steric effect of the guest enhances the deshielding of its 1H NMR signalsand (2) large affinity of the guest to the host minimized the deshielding of guest 1H NMR signals. Therefore, this supports why this effect is lower in the D series. On the other hand, the proton signals corresponding to ligand 6 (entries 24–26) do not show any significant changes, so neither the guest nor the host are affected. This reinforces the finding that the interaction takes place through the carboxylic acid.
Table 4. 1H NMR Data for the Selected Signals of the Ligands 1–6 at Several Concentrations and the Host at 2.5 mM Concentration
   δ 1H NMR (ppm) 
entry[guest] [mM]CC3-R mMH1H2Δδ H1/H2
1l-1 4.3881.488 
23 mM l-12.54.35121.48630.0365/0.0017
310 mM l-12.54.3111.44280.077/0.0452
43 mM d-12.54.36221.48650.0258/0.0015
510 mM d-12.54.3511.47180.037/0.0165
6l-2 4.29141.44 
73 mM l-22.54.28611.44130.0053/–0.0013
810 mM l-22.54.28081.44740.0106/–0.074
93 mM d-22.54.29051.44200.0009/–0.0020
1010 mM d-22.54.28661.44150.0048/–0.0015
11l-3 4.20861.0246/0.96 
123 mM l-32.54.2081.0375/0.97090.0006/–0.0129/–0.0109
1310 mM l-32.54.18151.0235/0.96040.0271/0.0011/–0.0004
143 mM d-32.54.20801.0369/0.96490.0006/–0.0123/–0.0049
1510 mM d-32.54.17651.0148/0.94610.0321/0.0098/0.0139
16l-4 4.2640.9836/0.9757 
173 mM l-42.54.2781.004/0.9917–0.014/–0.0204/–0.016
1810 mM l-42.54.2781.0098/0.9966–0.014/–0.0262/–0.0209
193 mM d-42.54.2780.9962–0.014/–0.0126/–0.0205
2010 mM d-42.54.2781.0036–0.014/–0.02/–0.0279
21l-5 4.352  
2210 mM l-52.54.344 0.008
2310 mM d-52.54.350 0.002
2410 mM S-6 4.9021.490 
2510 mM S-62.54.9111.491–0.007/–0.001
2610 mM R-62.54.9111.490–0.007/0.000
Figure 4 shows the 1H NMR spectra of the CC3-R in the presence of guest 1 in its L, R and racemic forms. There, we can observe that the material CC3-R is not only a good support of chiral column for gas and liquid chromatography for the separation of enantiomeric mixtures as has been shown in previous studies, but it could also act as a chiral solvating agent (CSA) for poorly impeded N-BOC-amino acids and α-hydroxy acids. Therefore, this material would have an even wider application than that reported so far.

Figure 4

Figure 4. 1H NMR region for the corresponding methyl group signal of ligand 1 at 3 mM and the host at 2.5 mM; (a) rac-1; (b) S-1; (c) R-1; and (d) isolated S-1.

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A variety of NMR pulse sequences that allow the investigation of diffusion constants in solution have been applied to understand the host–guest interaction and diffusion in CC3-R. On the basis of such experiments, it is possible to discriminate compounds in mixtures according to their diffusion properties. This diffusion experiment has been previously successfully applied to deconvolute compound mixtures and to detect molecular association processes. (48−53) Although the main difficulty is that for the detection of changes in the diffusion constant of a ligand that binds to a protein, it is necessary that a significant amount of the ligand is bound to the protein on the time average. Diffusion experiments have been proven to be a valuable tool for characterizing molecular interactions between small and intermediate size molecules. Therefore, PGSE diffusion NMR has been also applied to the several samples. Then, the preparation of different samples of the selected guests with and without CC3-R present was carried out and then the comparison of the corresponding diffusion constant should give information about the binding affinity.
Table 5 shows the data obtained from the diffusion measurements on all guests in the samples at a concentration of 2.5 and 3 mM for the host and guest, respectively. As in previous studies, the case of lactic acid has been the most relevant, confirming that the enantiomer L has a slightly higher affinity than the D enantiomer toward the guest CC3-R. The changes in the diffusion coefficients and hydrodynamic radius are very clear between free host and host–guest. In fact, more than 50% of l-lactic acid is interacting with the host material. On the other hand, changes in the values of the diffusion coefficients and hydrodynamic radii for the other guests 2–6 are not very significant, being at best 21% host, l-2, which interacts with the guest very far from the values determined for l-1.
Table 5. Diffusion Data for the Selected Guests 1–7 with and without the Host
entry[guest] [3 mM]COF [2.5 mM]D [10–10 m2 s–1]rH [Å]guest free/guest inside
1 X6.68.1 
2l-1 22.32.4 
3l-1X13.53.951.6/48.4
4d-1X14.23.756.1/43.9
5l-2 143.8 
6l-2X12.44.378.2/21.8
7d-2X12.84.283.8/16.2
8l-3 13.14.1 
9l-3X12.34.387.7/12.3
10d-3X12.84.291.4/8.6
11l-4 13.14.1 
12l-4X12.24.486.2/13.8
13d-4X12.44.389.2/10.8
14l-5 153.5 
15l-5X14.53.794/6
16d-5X14.93.698.8/1.2
17S-6 22.32.4 
18S-6X21.12.595.5/4.5
19R-6X21.62.594.9/5.1
Finally, saturation-transfer NMR spectroscopy, STD, has been used for many years to characterize binding in tightly bound ligand–receptor complexes. At the same time, it was also shown that STD NMR is an excellent technique for determining the binding epitope of the ligand, information that is of prime importance for the directed development of drugs. (54) On the basis of that, STD experiments were carried out over several samples because it is a suitable experiment to probe SAR by NMR spectroscopy and also to determine association/dissociation contacts. However, STD experiments were not successful because the size of the host is too small for applying these experiments being applicable for systems larger than 15 000 kDa.

DFT Study of Host–Guest Interactions

The interaction of guest molecules 1 and 2 and benzoic acid with a POC of composition N12C72H84 as a model of the CC3-R material were theoretically investigated by means of DFT calculations. After full geometry optimization without any restriction, the organic cage maintains its tetrahedral symmetry as well as its window size and shape. The interaction of lactic acid 1 with the CC3-R model involves a strong hydrogen bond between the proton of the carboxylic group of the guest molecule and the imine N atom of the host POC and, in some cases, an additional weaker interaction between the C═O oxygen atom of lactic acid and a neighboring imine H1 atom (see Figure 5). In addition, the same type of adsorption is found for the guest molecule alanine 2. For both molecules, different adsorption complexes can be obtained depending on the relative orientation of the methyl group of the guest with respect to the organic skeleton of the host COF. All calculated interaction energies range from −60 to −80 kJ/mol, and the relative stability of the two most stable orientations for each enantiomer (labeled as a or b in Figure 5 and Table 6) differ by 15 kJ/mol at most. It is also important to remark that the interaction of the CC3-R model with the L enantiomer is in both systems slightly stronger than that with the D enantiomer, in agreement with the results from the NMR study.

Figure 5

Figure 5. DFT structures for the interaction CC3-R–guest; l-1 and d-1; l-2 and d-2.

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Table 6. DFT Data for the Host–Guest Systems Depicted in the Figure 5
entryguestEint [kJ/mol]rH–H1 [Å]rH–H2 [Å]rH–H3 [Å]
1l-1a–76.92.5193.5402.838
2l-1b–61.63.9334.1914.669
3d-1a–74.82.9233.6333.414
4d-1b–69.32.4643.7642.671
5l-2a–78.92.5483.4512.837
6l-2b–73.02.4503.5492.836
7d-2a–72.72.2653.6312.512
8d-2b–63.72.5523.7882.654
Finally, the interaction of benzoic acid with the CC3-R model by π interaction between aromatic rings was also considered and compared with the previously described carboxylic group-imine bonding (see Figure S83 of the Supporting Information). The calculated interaction energies, −44.6 and −77.4 kJ/mol for the π and imine bonding, respectively, confirm the preferential interaction through the carboxylic group.
Changes in the chemical shifts and an increase in signal line widths are observed in the 1H NMR spectrum of the host for N-BOC-amino acids and especially with the α-hydroxy acid. This effect implies a greater deshielding of signals of CC3-R toward those hosts with more affinity. When the alcohol 6 was studied, no change in the chemical shift of the signals with respect to the isolated species was observed. This behavior evidences the interactions between both systems through the carboxylic group. Likewise, the 1H NMR signals of the hosts in the presence of the guest also suffer displacements of the signals with respect to the free compound. Further shielding of such signals is related to a greater affinity toward the guest by the host. Other functional groups, such as free amino acids, were not able to be studied because CC3-R is only slightly soluble in CD2Cl2 while free amino acids are only soluble in D2O or polar organic solvent. In the study carried out by means of carbon NMR on the signals of the CC3-R imine and aromatic, it has been shown that this nucleus undergoes very small changes of magnitude and therefore does not provide great information as sensor of the interaction process. However, the nitrogen NMR provides a great deal of information and could be considered an indicator of the degree of host–guest interaction.
In addition, NMR diffusion can also be established as a very useful tool to identify that molecules interact more strongly with these chiral boxes. All these results were supported with theoretical calculations. Finally, the possibility of using these materials as chiral resolution agents by NMR has been opened.

Conclusion

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In summary, the study carried out on the CC3-R systems, through NMR and supported by theoretical calculations, has allowed to elucidate and to understand the interactions of these systems with different hosts. In addition, it becomes clear that NMR is a very useful technique to identify such mechanism of action, guest–host interaction, in enantiomeric separation processes, just as it has been in biology. Finally, it has been determined that such materials can be used as enantiomeric resolution agents by NMR. Currently, we are working to develop chiral materials that act on CSA but with a greater capacity for the determination of enantiomeric excesses.

Supporting Information

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The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.jpcc.8b05069.

  • Experimental procedures; spectral and computational details; and cartesian coordinates for all optimized structures (PDF)

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Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system: http://pubs.acs.org/page/copyright/permissions.html.

Author Information

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  • Corresponding Authors
  • Authors
    • Sara Sáez-Ferre - Instituto de Tecnología Química, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas (UPV-CSIC), Avda. de los Naranjos s/n, 46022 Valencia, Spain
    • Mercedes Boronat - Instituto de Tecnología Química, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas (UPV-CSIC), Avda. de los Naranjos s/n, 46022 Valencia, Spain
    • Ángel Cantín - Instituto de Tecnología Química, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas (UPV-CSIC), Avda. de los Naranjos s/n, 46022 Valencia, Spain
  • Notes
    The authors declare no competing financial interest.

Acknowledgments

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Program Severo Ochoa SEV-2016-0683 is gratefully acknowledged. S.S-F. thanks MEC for his Severo Ochoa Grant SPV-2013-067884, P.O.-B. thanks MEC for his Ramón y Cajal contract RYC-2014-16620. M.B. and F.R. thank the financial support by the Spanish Government (MAT2017-82288-C2-1-P and MAT2015-71842-P). The authors thank the MULTY2HYCAT (EU-Horizon 2020 funded project under grant agreement no. 720783). The Electron Microscopy Service of the UPV is acknowledged for their help in sample characterization.

References

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    Covalent org. frameworks, COFs, and their derived sub-groups based on auto-assembly of exclusively arom. units, PAFs, are emerging into the advanced materials field due to their high free porous vol., structural regularity, robustness, hydrothermal stability, and functional variety. They present high gas uptake capacities and presence of stabilized active functions in the framework. This together with charged low-d. structures combined with their organization through π-conjugated system arrays, open the possibilities of COFs and PAFs to be used as effective materials for adsorption, selective sepn. and catalysis, and in nanotechnol. applications. This review will be focused on self-assembly synthesis mechanisms, physico-chem. characteristics, and applications of this class of promising covalent porous org. structures, out looking their possible future approaches and perspectives.
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  14. 14
    Das, S.; Heasman, P.; Ben, T.; Qiu, S. Porous Organic Materials: Strategic Design and Structure-Function Correlation. Chem. Rev. 2017, 117, 1515– 1563,  DOI: 10.1021/acs.chemrev.6b00439
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    Porous organic material strategic design and structure-function correlation
    Das, Saikat; Heasman, Patrick; Ben, Teng; Qiu, Shilun
    Chemical Reviews (Washington, DC, United States) (2017), 117 (3), 1515-1563CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)
    Porous org. materials have garnered colossal interest with the scientific fraternity due to their excellent gas sorption performances, catalytic abilities, energy storage capacities, and other intriguing applications. This review encompasses the recent significant breakthroughs and the conventional functions and practices in the field of porous org. materials to find useful applications and imparts a comprehensive understanding of the strategic evolution of the design and synthetic approaches of porous org. materials with tunable characteristics. We present an exhaustive anal. of the design strategies with special emphasis on the topologies of cryst. and amorphous porous org. materials. In addn. to elucidating the structure-function correlation and state-of-the-art applications of porous org. materials, we address the challenges and restrictions that prevent us from realizing porous org. materials with tailored structures and properties for useful applications.
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  15. 15
    Dawson, R.; Cooper, A. I.; Adams, D. J. Nanoporous organic polymer networks. Prog. Polym. Sci. 2012, 37, 530– 563,  DOI: 10.1016/j.progpolymsci.2011.09.002
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    Nanoporous organic polymer networks
    Dawson, Robert; Cooper, Andrew I.; Adams, Dave J.
    Progress in Polymer Science (2012), 37 (4), 530-563CODEN: PRPSB8; ISSN:0079-6700. (Elsevier Ltd.)
    A review. Nanoporous org. polymer networks are a class of materials consisting solely of the lighter elements in the periodic table. These materials have potential uses in areas such as storage, sepn., and catalysis. Here, we review the different classes of nanoporous polymer networks including covalent org. frameworks, hypercrosslinked polymers, conjugated microporous polymers, and polymers of intrinsic microporosity. The growing variety in synthetic routes to these materials allows a range of different polymer networks to be formed, including cryst. and amorphous structures. It is also possible to incorporate many different kinds of functional groups in a modular fashion. So far, most networks have been examd. from the perspective of gas sorption, and this area is discussed critically and in depth in this review. The use of nanoporous org. polymers for applications such as catalysis and sepns. is an important developing area, and we discuss recent developments as well as highlighting potential future opportunities.
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    Tan, L.; Tan, B. Hypercrosslinked porous polymer materials: design, synthesis, and applications. Chem. Soc. Rev. 2017, 46, 3322– 3356,  DOI: 10.1039/c6cs00851h
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    16
    Hypercrosslinked porous polymer materials: design, synthesis, and applications
    Tan, Liangxiao; Tan, Bien
    Chemical Society Reviews (2017), 46 (11), 3322-3356CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)
    A review. Hypercrosslinked polymers (HCPs) are a series of permanent microporous polymer materials initially reported by Davankov, and have received an increasing level of research interest. In recent years, HCPs have experienced rapid growth due to their remarkable advantages such as diverse synthetic methods, easy functionalization, high surface area, low cost reagents and mild operating conditions. Judicious selection of monomers, appropriate length crosslinkers and optimized reaction conditions yielded a well-developed polymer framework with an adjusted porous topol. Post fabrication of the as developed network facilitates the incorporation of various chem. functionalities that may lead to interesting properties and enhance the selection toward a specific application. To date, numerous HCPs have been prepd. by post-crosslinking polystyrene-based precursors, one-step self-polycondensation or external crosslinking strategies. The advent of these methodologies has prompted researchers to construct well-defined porous polymer networks with customized micromorphol. and functionalities. In this review, we describe not only the basic synthetic principles and strategies of HCPs, but also the advancements in the structural and morphol. study as well as the frontiers of potential applications in energy and environmental fields such as gas storage, carbon capture, removal of pollutants, mol. sepn., catalysis, drug delivery, sensing, etc.
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    Bojdys, M. J.; Hasell, T.; Severin, N.; Jelfs, K. E.; Rabe, J. P.; Cooper, A. I. Porous organic cage crystals: characterising the porous crystal surface. Chem. Commun. 2012, 48, 11948– 11950,  DOI: 10.1039/c2cc36602a
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    17
    Porous organic cage crystals: characterizing the porous crystal surface
    Bojdys, Michael J.; Hasell, Tom; Severin, Nikolai; Jelfs, Kim E.; Rabe, Juergen P.; Cooper, Andrew I.
    Chemical Communications (Cambridge, United Kingdom) (2012), 48 (98), 11948-11950CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)
    The characterization of porous cryst. solids often relies on single crystal x-ray diffraction, which does not give direct information about the surface of the material. Here, crystals of a porous org. cage, CC3-R, were studied by at. force microscopy and shown to possess two distinct gas-solid interfaces, proving that the bulk crystal structure is preserved at the porous crystal surface.
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  18. 18
    Tozawa, T.; Jones, J. T. A.; Swamy, S. I.; Jiang, S.; Adams, D. J.; Shakespeare, S.; Clowes, R.; Bradshaw, D.; Hasell, T.; Chong, S. Y.; Tang, C.; Thompson, S.; Parker, J.; Trewin, A.; Bacsa, J.; Slawin, A. M. Z.; Steiner, A.; Cooper, A. I. Porous organic cages. Nat. Mater. 2009, 8, 973– 978,  DOI: 10.1038/nmat2545
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    18
    Porous organic cages
    Tozawa, Tomokazu; Jones, James T. A.; Swamy, Shashikala I.; Jiang, Shan; Adams, Dave J.; Shakespeare, Stephen; Clowes, Rob; Bradshaw, Darren; Hasell, Tom; Chong, Samantha Y.; Tang, Chiu; Thompson, Stephen; Parker, Julia; Trewin, Abbie; Bacsa, John; Slawin, Alexandra M. Z.; Steiner, Alexander; Cooper, Andrew I.
    Nature Materials (2009), 8 (12), 973-978CODEN: NMAACR; ISSN:1476-1122. (Nature Publishing Group)
    Porous materials are important in a wide range of applications including mol. sepns. and catalysis. Covalently bonded org. cages can assemble into cryst. microporous materials. The porosity is prefabricated and intrinsic to the mol. cage structure, as opposed to being formed by noncovalent self-assembly of nonporous sub-units. The three-dimensional connectivity between the cage windows is controlled by varying the chem. functionality such that either nonporous or permanently porous assemblies can be produced. Surface areas and gas uptakes for the latter exceed comparable mol. solids. One of the cages can be converted by recrystn. to produce either porous or nonporous polymorphs with apparent Brunauer-Emmett-Teller surface areas of 550 and 23 m2 g-1, resp. These results suggest design principles for responsive porous org. solids and for the modular construction of extended materials from prefabricated mol. pores.
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  19. 19
    Chen, L.; Reiss, P. S.; Chong, S. Y.; Holden, D.; Jelfs, K. E.; Hasell, T.; Little, M. A.; Kewley, A.; Briggs, M. E.; Stephenson, A.; Thomas, K. M.; Armstrong, J. A.; Bell, J.; Busto, J.; Noel, R.; Liu, J.; Strachan, D. M.; Thallapally, P. K.; Cooper, A. I. Separation of rare gases and chiral molecules by selective binding in porous organic cages. Nat. Mater. 2014, 13, 954– 960,  DOI: 10.1038/nmat4035
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    Separation of rare gases and chiral molecules by selective binding in porous organic cages
    Chen, Linjiang; Reiss, Paul S.; Chong, Samantha Y.; Holden, Daniel; Jelfs, Kim E.; Hasell, Tom; Little, Marc A.; Kewley, Adam; Briggs, Michael E.; Stephenson, Andrew; Thomas, K. Mark; Armstrong, Jayne A.; Bell, Jon; Busto, Jose; Noel, Raymond; Liu, Jian; Strachan, Denis M.; Thallapally, Praveen K.; Cooper, Andrew I.
    Nature Materials (2014), 13 (10), 954-960CODEN: NMAACR; ISSN:1476-1122. (Nature Publishing Group)
    A porous org. cage mol. having unprecedented performance in the solid state for the sepn. of rare gases, such as krypton and xenon, is reported. The selectivity arises from a precise size match between the rare gas and the org. cage cavity, as predicted by mol. simulations. Breakthrough expts. demonstrate real practical potential for the sepn. of krypton, xenon and radon from air at concns. of only a few ppm. Selective binding of chiral org. mols. such as 1-phenylethanol is also demonstrated, suggesting applications in enantioselective sepn.
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  20. 20
    Briggs, M. E.; Slater, A. G.; Lunt, N.; Jiang, S.; Little, M. A.; Greenaway, R. L.; Hasell, T.; Battilocchio, C.; Ley, S. V.; Cooper, A. I. Dynamic flow synthesis of porous organic cages. Chem. Commun. 2015, 51, 17390– 17393,  DOI: 10.1039/c5cc07447a
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    Dynamic flow synthesis of porous organic cages
    Briggs, Michael E.; Slater, Anna G.; Lunt, Neil; Jiang, Shan; Little, Marc A.; Greenaway, Rebecca L.; Hasell, Tom; Battilocchio, Claudio; Ley, Steven V.; Cooper, Andrew I.
    Chemical Communications (Cambridge, United Kingdom) (2015), 51 (98), 17390-17393CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)
    The dynamic covalent synthesis of two imine-based porous org. cages was successfully transferred from batch to continuous flow. The same flow reactor was then used to scramble the constituents of these two cages in differing ratios to form cage mixts. Preparative HPLC purifn. of one of these mixts. allowed rapid access to a desymmetrised cage mol.
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    Jiang, S.; Jones, J. T. A.; Hasell, T.; Blythe, C. E.; Adams, D. J.; Trewin, A.; Cooper, A. I. Porous organic molecular solids by dynamic covalent scrambling. Nat. Commun. 2011, 2, 207,  DOI: 10.1038/ncomms1207
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    21
    Porous organic molecular solids by dynamic covalent scrambling
    Jiang Shan; Jones James T A; Hasell Tom; Blythe Charlotte E; Adams Dave J; Trewin Abbie; Cooper Andrew I
    Nature communications (2011), 2 (), 207 ISSN:.
    The main strategy for constructing porous solids from discrete organic molecules is crystal engineering, which involves forming regular crystalline arrays. Here, we present a chemical approach for desymmetrizing organic cages by dynamic covalent scrambling reactions. This leads to molecules with a distribution of shapes which cannot pack effectively and, hence, do not crystallize, creating porosity in the amorphous solid. The porous properties can be fine tuned by varying the ratio of reagents in the scrambling reaction, and this allows the preparation of materials with high gas selectivities. The molecular engineering of porous amorphous solids complements crystal engineering strategies and may have advantages in some applications, for example, in the compatibilization of functionalities that do not readily cocrystallize.
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    Little, M. A.; Chong, S. Y.; Schmidtmann, M.; Hasell, T.; Cooper, A. I. Guest control of structure in porous organic cages. Chem. Commun. 2014, 50, 9465– 9468,  DOI: 10.1039/c4cc04158e
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    Guest control of structure in porous organic cages
    Little, Marc A.; Chong, Samantha Y.; Schmidtmann, Marc; Hasell, Tom; Cooper, Andrew I.
    Chemical Communications (Cambridge, United Kingdom) (2014), 50 (67), 9465-9468CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)
    Two porous org. cages with different thermodn. polymorphs were induced by co-solvents to interchange their crystal packing modes, thus achieving guest-mediated control over solid-state porosity. In situ crystallog. allows the effect of the co-solvent guests on these structural interconversions to be understood.
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    Kewley, A.; Stephenson, A.; Chen, L.; Briggs, M. E.; Hasell, T.; Cooper, A. I. Porous organic cages for gas chromatography separations. Chem. Mater. 2015, 27, 3207– 3210,  DOI: 10.1021/acs.chemmater.5b01112
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    23
    Porous Organic Cages for Gas Chromatography Separations
    Kewley, Adam; Stephenson, Andrew; Chen, Linjiang; Briggs, Michael E.; Hasell, Tom; Cooper, Andrew I.
    Chemistry of Materials (2015), 27 (9), 3207-3210CODEN: CMATEX; ISSN:0897-4756. (American Chemical Society)
    Chromatog. is an important process for characterizing and purifying org. mols., but some mixts. remain challenging to sep. The authors report the 1st use of a soln.-processable porous org. cage mol., (I, CC3), as a stationary phase for gas chromatog. Capillary columns were coated with CC3 using a simple, static coating method. These columns are versatile and can sep. alkanes, arom. mixts., and chiral mols. Atomistic simulations indicate that the efficient shape sorting of branched hexane isomers by CC3 results from a combination of kinetic diffusion and surface-interaction effects.
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    Briggs, M. E.; Cooper, A. I. A perspective on the synthesis, purification, and characterization of porous organic cages. Chem. Mater. 2017, 29, 149– 157,  DOI: 10.1021/acs.chemmater.6b02903
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    24
    A Perspective on the Synthesis, Purification, and Characterization of Porous Organic Cages
    Briggs, Michael E.; Cooper, Andrew I.
    Chemistry of Materials (2017), 29 (1), 149-157CODEN: CMATEX; ISSN:0897-4756. (American Chemical Society)
    A review with authors data. Porous org. cages present many opportunities in functional materials chem., but the synthetic challenges for these mol. solids are somewhat different from those faced in the areas of metal-org. frameworks, covalent-org. frameworks, or porous polymer networks. Here, we highlight the practical methods that we have developed for the design, synthesis, and characterization of imine porous org. cages using CC1 and CC3 as examples. The key points are transferable to other cages, and this perspective should serve as a practical guide to researchers who are new to this field.
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    Xie, S.-M.; Zhang, J.-H.; Fu, N.; Wang, B.-J.; Chen, L.; Yuan, L.-M. A chiral porous organic cage for molecular recognition using gas chromatography. Anal. Chim. Acta 2016, 903, 156– 163,  DOI: 10.1016/j.aca.2015.11.030
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    A chiral porous organic cage for molecular recognition using gas chromatography
    Xie, Sheng-Ming; Zhang, Jun-Hui; Fu, Nan; Wang, Bang-Jin; Chen, Ling; Yuan, Li-Ming
    Analytica Chimica Acta (2016), 903 (), 156-163CODEN: ACACAM; ISSN:0003-2670. (Elsevier B.V.)
    Mol. org. cages as shape-persistent org. mols. with permanent and accessible cavities have attracted a lot of interest because of their importance as host-guest systems. Herein, the authors report a chiral porous org. cage (POC) CC9 dild. with a polysiloxane OV-1701 to fabricate a CC9-coated capillary column, which was used for the high-resoln. gas chromatog. sepn. of org. compds., including positional isomers and racemates. On the porous org. cage CC9-coated capillary column, a large no. of racemic compds. such as chiral alcs., esters, ethers and epoxides can be resolved without derivatization. By comparing the chiral recognition ability of the CC9-coated column with the com. available β-DEX 120 column and the POC CC3-R coated column recently reported by the authors' group, the CC9-coated column offered good resoln. during the sepn. of some racemates, that were not sepd. using the β-DEX 120 column or POC CC3-R coated column. Therefore, the CC9-coated column can be complementary to the β-DEX 120 column and CC3-R coated column. The CC9-coated column exhibited great potential for application in the sepn. of positional isomers and enantiomers with great selectivity, high resoln. and good reproducibility.
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    Zhang, J.-H.; Xie, S.-M.; Chen, L.; Wang, B.-J.; He, P.-G.; Yuan, L.-M. Homochiral porous organic cage with high selectivity for the separation of racemates in gas chromatography. Anal. Chem. 2015, 87, 7817– 7824,  DOI: 10.1021/acs.analchem.5b01512
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    Homochiral Porous Organic Cage with High Selectivity for the Separation of Racemates in Gas Chromatography
    Zhang, Jun-Hui; Xie, Sheng-Ming; Chen, Ling; Wang, Bang-Jin; He, Pin-Gang; Yuan, Li-Ming
    Analytical Chemistry (Washington, DC, United States) (2015), 87 (15), 7817-7824CODEN: ANCHAM; ISSN:0003-2700. (American Chemical Society)
    Porous org. mol. cages as a new type of porous materials have attracted a tremendous attention for their potential applications in recent years. Here the authors report the use of a homochiral porous org. cage (POC) (CC3-R) dild. with a polysiloxane (OV-1701) as a stationary phase for high-resoln. gas chromatog. (GC) with excellent enantioselectivity. A large no. of optical isomers were resolved without derivatization, including chiral alcs., diols, amines, alc. amines, esters, ketones, ethers, halohydrocarbons, org. acids, amino acid Me esters, and sulfoxides. Compared with com. β-DEX 120 and Chirasil-L-Val columns, the CC3-R coated capillary column offered more preeminent enantioselectivity. CC3-R also exhibits good selectivity for the sepn. of isomers, linear alkanes, alcs., and arom. hydrocarbons. The excellent resoln. ability, repeatability, and thermal stability make CC3-R a promising candidate as a novel stationary phase for GC. The study described herein first proves useful com. Also porous org. mol. materials will become more attractive in sepn. science.
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    Stilbs, P. Fourier transform pulsed-gradient spin-echo studies of molecular diffusion. Prog. Nucl. Magn. Reson. Spectrosc. 1987, 19, 1– 45,  DOI: 10.1016/0079-6565(87)80007-9
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    Fourier transform pulsed-gradient spin-echo studies of molecular diffusion
    Stilbs, Peter
    Progress in Nuclear Magnetic Resonance Spectroscopy (1987), 19 (1), 1-45CODEN: PNMRAT; ISSN:0079-6565.
    A review with 193 refs. is given on NMR methods (esp. Fourier-transform, pulsed-field-gradient, spin-echo NMR) in measuring mol. diffusion (self-diffusion, mutual diffusion, and multicomponent diffusion) in various types of systems (including liqs., liq. mixts., polymer and polyelectrolyte solns., gels, surfactant aq. solns., and emulsions).
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    Zhao, Y.; Truhlar, D. G. The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals. Theor. Chem. Acc. 2008, 120, 215– 241,  DOI: 10.1007/s00214-007-0310-x
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    The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals
    Zhao, Yan; Truhlar, Donald G.
    Theoretical Chemistry Accounts (2008), 120 (1-3), 215-241CODEN: TCACFW; ISSN:1432-881X. (Springer GmbH)
    We present two new hybrid meta exchange-correlation functionals, called M06 and M06-2X. The M06 functional is parametrized including both transition metals and nonmetals, whereas the M06-2X functional is a high-nonlocality functional with double the amt. of nonlocal exchange (2X), and it is parametrized only for nonmetals. The functionals, along with the previously published M06-L local functional and the M06-HF full-Hartree-Fock functionals, constitute the M06 suite of complementary functionals. We assess these four functionals by comparing their performance to that of 12 other functionals and Hartree-Fock theory for 403 energetic data in 29 diverse databases, including ten databases for thermochem., four databases for kinetics, eight databases for noncovalent interactions, three databases for transition metal bonding, one database for metal atom excitation energies, and three databases for mol. excitation energies. We also illustrate the performance of these 17 methods for three databases contg. 40 bond lengths and for databases contg. 38 vibrational frequencies and 15 vibrational zero point energies. We recommend the M06-2X functional for applications involving main-group thermochem., kinetics, noncovalent interactions, and electronic excitation energies to valence and Rydberg states. We recommend the M06 functional for application in organometallic and inorganometallic chem. and for noncovalent interactions.
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    Krishnan, R.; Binkley, J. S.; Seeger, R.; Pople, J. A. Self-consistent molecular orbital methods. XX. A basis set for correlated wave functions. J. Chem. Phys. 1980, 72, 650– 654,  DOI: 10.1063/1.438955
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    Self-consistent molecular orbital methods. XX. A basis set for correlated wave functions
    Krishnan, R.; Binkley, J. S.; Seeger, R.; Pople, J. A.
    Journal of Chemical Physics (1980), 72 (1), 650-4CODEN: JCPSA6; ISSN:0021-9606.
    A contracted Gaussian basis set (6-311G**) is developed by optimizing exponents and coeffs. at the Moller-Plesset (MP) second-order level for the ground states of first-row atoms. This has a triple split in the valence s and p shells together with a single set of uncontracted polarization functions on each atom. The basis is tested by computing structures and energies for some simple mols. at various levels of MP theory and comparing with expt.
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    Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Petersson, G. A.; Nakatsuji, H.; Gaussian 09, Revision C.01; Gaussian, Inc.: Wallingford CT, 2009.
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    Stejskal, E. O.; Tanner, J. E. Spin Diffusion Measurements: Spin Echoes in the Presence of a Time-Dependent Field Gradient. J. Chem. Phys. 1965, 42, 288– 292,  DOI: 10.1063/1.1695690
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    Spin diffusion measurements: spin echoes in the presence of a time-dependent field gradient
    Stejskal, E. O.; Tanner, J. E.
    Journal of Chemical Physics (1965), 42 (1), 288-92CODEN: JCPSA6; ISSN:0021-9606.
    A derivation is given of the effect of a time-dependent magnetic field gradient on the spin-echo expt., particularly in the presence of spin diffusion. There are several reasons for preferring certain kinds of time-dependent magnetic field gradients to the more usual steady gradient. If the gradient is reduced during the radio-frequency pulses, H1 need not be particularly large; if the gradient is small at the time of the echo, the echo will be broad and its amplitude easy to measure. Both of these relaxations of restrictions on the measurement of diffusion coeffs. by the spin-echo technique serve to extend its range of applicability. A pulsed gradient can be recommended when it is crit. to define the precise time period over which diffusion is being measured. The theoretical expression derived was verified exptl. for several choices of time-dependent magnetic field gradient. An app. is described suitable for the production of pulsed gradients with amplitudes as large as 100 gauss cm. The diffusion coeff. of dry glycerol at 26° ± 1° is (2.5 ± 0.2) × 10-3 cm.2/sec., a value smaller than can ordinarily be measured by the steady gradient method.
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    Use of the stimulated echo in NMR diffusion studies
    Tanner, John E.
    Journal of Chemical Physics (1970), 52 (5), 2523-6CODEN: JCPSA6; ISSN:0021-9606.
    The stimulated echo in a three-radio-frequency-pulse expt. is useful in extending the range of measurement of diffusion coeffs. to more viscous substances or the measurement of barrier sepns. to wider spacings in systems where the diffusing substance has T1 > T2. The spin-echo attenuation due to self-diffusion is derived for the general case of a time-dependent field gradient, and the result is found exptl. to be correct for the special case of a field gradient applied in 2 equal, square pulse.
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    Johnson, C. S. Diffusion ordered nuclear magnetic resonance spectroscopy: principles and applications. Magn. Reson. Spectrosc. 1999, 34, 203– 256,  DOI: 10.1016/s0079-6565(99)00003-5
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    Diffusion ordered nuclear magnetic resonance spectroscopy: principles and applications
    Johnson, C. S., Jr.
    Progress in Nuclear Magnetic Resonance Spectroscopy (1999), 34 (3,4), 203-256CODEN: PNMRAT; ISSN:0079-6565. (Elsevier Science B.V.)
    A review with 146 refs.
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    Chen, A.; Wu, D.; Johnson, C. S. Determination of molecular weight distributions for polymers by diffusion-ordered NMR. J. Am. Chem. Soc. 1995, 117, 7965– 7970,  DOI: 10.1021/ja00135a015
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    Determination of Molecular Weight Distributions for Polymers by Diffusion-Ordered NMR
    Chen, Aidi; Wu, Donghui; Johnson, Charles S., Jr.
    Journal of the American Chemical Society (1995), 117 (30), 7965-70CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    Diffusion-ordered NMR spectroscopy, a technique based on pulsed field gradient NMR (PFGNMR), was used to characterize mol. wt. distributions for samples of poly(ethylene oxide) in D2O. The distribution of diffusion coeffs. G(D) was obtained by anal. of PFGNMR data with a modified version of the well-known constrained regularization program CONTIN. Regularization was considerably improved for broad distributions by setting the wts. cm in CONTIN's quadrature formula equal to (Dm/Dmax)xm, where Dmax is the diffusion coeff. corresponding to the max. in G(Dm)Dm and m is an index. Here xm varies linearly from +2 to -2 with log(Dm) across the distribution. This amts. to enhancing low amplitude regions of G(D)D during anal. The estd. distribution was then converted to the mass weighted distribution of mol. wts. by means of the relation D = 10-7.62 M-0.62 (with D in units of m2 s-1) obtained from expts. on monodisperse ref. stds. In this study spin relaxation rates were independent of mol. wts. and intermol. averaging effects were insignificant. As an illustration, mol. wt. distributions were detd. for two broadly distributed samples. The no. and wt. av. mol. wts. and the polydispersities agreed well with values provided by the manufacturer when the PFGNMR data sets had signal-to-noise ratios greater than 500.
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    Avram, L.; Cohen, Y. Diffusion NMR of molecular cages and capsules. Chem. Soc. Rev. 2015, 44, 586– 602,  DOI: 10.1039/c4cs00197d
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    Diffusion NMR of molecular cages and capsules
    Avram, Liat; Cohen, Yoram
    Chemical Society Reviews (2015), 44 (2), 586-602CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)
    A review. In the last decade diffusion NMR and diffusion ordered spectroscopy (DOSY) have become important anal. tools for the characterization of supramol. systems in soln. Diffusion NMR can be used to glean information on the (effective) size and shape of mol. species, as well as to probe inter-mol. interactions and can be used to est. the assocn. const. (Ka) of a complex. In addn., the diffusion coeff., as obtained from diffusion NMR, is a much more intuitive parameter than the chem. shift for probing self-assocn., aggregation and inter-mol. interactions. The diffusion coeff. may be an even more important anal. parameter in systems in which the formed supramol. entity has the same symmetry as its building units, when there is a large change in the mol. wt., where many mol. species are involved in the formation of the supramol. systems, and when proton transfer may occur which, in turn, may affect the chem. shift. Some of the self-assembled mol. capsules and cages prepd. in the last decade represent such supramol. systems and in the present review, following a short introduction on diffusion NMR, we survey the contribution of diffusion NMR and DOSY in the field of mol. containers and capsules. We will 1st focus on the role played by diffusion NMR in the field of H-bond driven self-assembled capsules. We then survey the contributions of diffusion NMR and DOSY to the study and characterization of metal-ligand cages and capsules. Finally, we describe a few recent applications of diffusion NMR in the field of hydrophobic, electrostatic and covalent containers.
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    Åslund, I.; Nowacka, A.; Nilsson, M.; Topgaard, D. Filter-exchange PGSE NMR determination of cell membrane permeability. J. Magn. Reson. 2009, 200, 291– 295,  DOI: 10.1016/j.jmr.2009.07.015
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    Filter-exchange PGSE NMR determination of cell membrane permeability
    Aslund Ingrid; Nowacka Agnieszka; Nilsson Markus; Topgaard Daniel
    Journal of magnetic resonance (San Diego, Calif. : 1997) (2009), 200 (2), 291-5 ISSN:.
    A new PGSE NMR sequence is introduced for measuring diffusive transport across the plasma membrane of living cells. A "diffusion filter" and a variable mixing time precedes a standard PGSE block for diffusion encoding of the NMR signal. The filter is a PGSE block optimized for selectively removing the magnetization of the extracellular water. With increasing mixing time the intra- and extracellular components approach their equilibrium fractional populations. The rate of exchange can be measured using only a few minutes of instrument time. Water exchange over the plasma membrane of starved yeast cells is studied in the temperature range +5 to +32 degrees C.
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    Occhipinti, P.; Griffiths, P. C. Quantifying diffusion in mucosal systems by pulsed-gradient spin-echo NMR. Adv. Drug Delivery Rev. 2008, 60, 1570– 1582,  DOI: 10.1016/j.addr.2008.08.006
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    Quantifying diffusion in mucosal systems by pulsed-gradient spin-echo NMR
    Occhipinti, Paola; Griffiths, Peter C.
    Advanced Drug Delivery Reviews (2008), 60 (15), 1570-1582CODEN: ADDREP; ISSN:0169-409X. (Elsevier B.V.)
    A review. Mucus, a thick and slimy secretion produced by submucosal cells, covers many epithelial surfaces in mammalian organs and prevents foreign particles that enter the body from accessing cells. However, the mucus layer also represents a potential barrier to the efficient delivery of nano-sized drug delivery systems (polyplexes, lipoplexes, particles) to the underlying mucosal epithelium. Many studies have considered the ability of nano-sized particles and polymers to diffuse within the mucosal network using a range of different techniques, including multiple-particle tracking (MPT), diffusion chamber studies and fluorescence recovery after photobleaching (FRAP). This review highlights the current understanding of the interaction of the diffusion of nano-sized structures within mucosal networks. Moreover, this article presents an introduction to pulsed-gradient spin-echo NMR (PGSE-NMR), a potential new tool to investigate the mobility of mol. species through mucosal networks and related biol. gels.
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    Marega, R.; Aroulmoji, V.; Dinon, F.; Vaccari, L.; Giordani, S.; Bianco, A.; Murano, E.; Prato, M. Diffusion-ordered NMR spectroscopy in the structural characterization of functionalized carbon nanotubes. J. Am. Chem. Soc. 2009, 131, 9086– 9093,  DOI: 10.1021/ja902728w
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    Diffusion-Ordered NMR Spectroscopy in the Structural Characterization of Functionalized Carbon Nanotubes
    Marega, Riccardo; Aroulmoji, Vincent; Dinon, Francesca; Vaccari, Lisa; Giordani, Silvia; Bianco, Alberto; Murano, Erminio; Prato, Maurizio
    Journal of the American Chemical Society (2009), 131 (25), 9086-9093CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    The emerging applications of functionalized C nanotubes (CNTs) in various research domains necessitate the use of many different anal. techniques to confirm their structural modifications in a fast and reliable manner. Thus far, NMR spectroscopy was not among the main tools for characterization of organically modified C nanostructures. 1H anal. is limited because the signals in these derivs. are typically weak and broad, resulting in uncertainties of a few ppm, and because of the strong interference of residual solvent signals. To overcome these limitations, the authors studied the applicability of 1H NMR spectroscopy based on gradient-edited diffusion pulse sequences (1-dimensional diffusion-ordered spectroscopy, DOSY) in the characterization of CNT derivs. In general, diffusion NMR expts. allow the sepn. of NMR signals of different species present in a mixt., according to their own diffusion coeffs., merging spectroscopy information with size anal. A selected set of CNT derivs. was synthesized and analyzed using 1-dimensional DOSY expts. by applying strong magnetic field gradients (up to 42.6 G cm-1). Colorimetric tests (i.e., Kaiser test) and TGA anal. support the NMR findings, which are related to isolated and/or bundled short SWNTs, from TEM and AFM characterization. The overall results show that the diffusion-based NMR spectroscopy is a fast and promising approach for the characterization of covalently modified CNT derivs.
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    Canzi, G.; Mrse, A. A.; Kubiak, C. P. Diffusion-ordered NMR spectroscopy as a reliable alternative to TEM for determining the size of gold nanoparticles in organic solutions. J. Phys. Chem. C 2011, 115, 7972– 7978,  DOI: 10.1021/jp2008557
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    Diffusion-Ordered NMR Spectroscopy as a Reliable Alternative to TEM for Determining the Size of Gold Nanoparticles in Organic Solutions
    Canzi, Gabriele; Mrse, Anthony A.; Kubiak, Clifford P.
    Journal of Physical Chemistry C (2011), 115 (16), 7972-7978CODEN: JPCCCK; ISSN:1932-7447. (American Chemical Society)
    Diffusion-ordered spectroscopy is used to det. gold nanoparticle sizes. Traditional characterization of nanoparticles has centered on imaging by electron microscopy and plasmon resonance absorption in UV-visible electronic spectra. The authors present a convenient method to characterize gold nanoparticles using diffusion-ordered NMR spectroscopy (DOSY). 2-dimensional DOSY NMR is used to calc. diffusion consts. and the diam. of solubilized gold nanoparticles capped with 1-dodecanethiol (C12) or 1-octanethiol (C8) in three deuterated solvents. The distributions of nanoparticle sizes strongly correlate with TEM image anal. C12 and C8 capped nanoparticle sizes are 4.6 and 2.7 nm by TEM as compared to ests. of 4.6 ± 0.3 and 2.5 ± 0.1 nm based on 2-dimensional DOSY NMR data. Reliable size characterization of nanoparticles with NMR active nuclei (1H in this study) in their protective groups (alkane thiols in this study) can be achieved by a widely available NMR method (DOSY) in place of electron microscopy.
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    Pascal, S. M.; Yamazaki, T.; Singer, A. U.; Kay, L. E.; Forman-Kay, J. D. Structural and dynamic characterization of the phosphotyrosine binding region of an Src homology 2 domain-phosphopeptide complex by NMR relaxation, proton exchange, and chemical shift approaches. Biochemistry 1995, 34, 11353– 11362,  DOI: 10.1021/bi00036a008
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    Structural and Dynamic Characterization of the Phosphotyrosine Binding Region of an Src Homology 2 Domain-Phosphopeptide Complex by NMR Relaxation, Proton Exchange, and Chemical Shift Approaches
    Pascal, Steven M.; Yamazaki, Toshio; Singer, Alex U.; Kay, Lewis E.; Forman-Kay, Julie D.
    Biochemistry (1995), 34 (36), 11353-62CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)
    Arginine side chains are often involved in protein-protein and protein-nucleic acid interactions. Due to a no. of factors, resonance assignment and detection of NOEs involving the arginine side chains via std. NMR techniques can be difficult. The authors present here an approach to characterization of the interaction between a phosphopeptide (pY1021) and four arginine residues that line the phosphotyrosine-binding pocket of the C-terminal SH2 domain of phospholipase C-γ1 (PLCC SH2). Previously published NOE data provide a partial description of this interaction, including contacts between the aliph. region of Arg 59 and the phosphotyrosine (pTyr) arom. ring. Further characterization has now been accomplished by using 15N and 13C NMR relaxation studies of arginine Νε and Cζ spins, resp., and proton exchange rates of arginine Hε nuclei. Differences between the chem. shifts of the arginine guanidino groups of the free SH2 domain in imidazole and phosphate buffers or in complex with pY1021 have provided insight into specific interactions with the phosphate and the arom. ring of the pTyr. The resulting data are consistent with the most stable hydrogen bonds to phosphate donated by the Arg 39 ε-NH and the two Arg 37 η-NH2 groups and with pTyr arom. ring interactions involving the Arg 39 and possibly the Arg 18 guanidino groups.
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    Yamazaki, T.; Pascal, S. M.; Singer, A. U.; Forman-Kay, J. D.; Kay, L. E. NMR pulse schemes for the sequence-specific assignment of arginine guanidino 15N and 1H chemical shifts in proteins. J. Am. Chem. Soc. 1995, 117, 3556– 3564,  DOI: 10.1021/ja00117a025
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    NMR Pulse Schemes for the Sequence-Specific Assignment of Arginine Guanidino 15N and 1H Chemical Shifts in Proteins
    Yamazaki, Toshio; Pascal, Steven M.; Singer, Alex U.; Forman-Kay, Julie D.; Kay, Lewis E.
    Journal of the American Chemical Society (1995), 117 (12), 3556-64CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    A family of 2D NMR expts. is presented for the sequence-specific assignment of arginine guanidino 1H and 15N chem. shifts on the basis of transfer of magnetization exclusively by scalar connectivities. Because of the potential for significant exchange with water at the ε and η positions along the side chain of arginine residues, care has been taken to minimize satn. and dephasing of water throughout the course of the pulse schemes. Attempts are made to minimize the effects of chem. exchange due to moderately slow rotation about the Nε-Cζ bond of arginine. The methods are demonstrated on a 1.5 mM sample of the C-terminal SH2 domain from phospholipase-Cγ1 in complex with a 12-residue phosphotyrosyl peptide comprising its high-affinity binding site in the platelet-derived growth factor receptor.
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    Feng, M.-H.; Philippopoulos, M.; MacKerell, A. D.; Lim, C. Structural Characterization of the Phosphotyrosine Binding Region of a High-Affinity SH2 Domain–Phosphopeptide Complex by Molecular Dynamics Simulation and Chemical Shift Calculations. J. Am. Chem. Soc. 1996, 118, 11265– 11277,  DOI: 10.1021/ja961530r
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    Structural Characterization of the Phosphotyrosine Binding Region of a High-Affinity SH2 Domain-Phosphopeptide Complex by Molecular Dynamics Simulation and Chemical Shift Calculations
    Feng, Ming-Hsiang; Philippopoulos, Marios; MacKerell, Alexander D., Jr.; Lim, Carmay
    Journal of the American Chemical Society (1996), 118 (45), 11265-11277CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    Three mol. dynamics simulations of the free, phosphate ion-bound and phosphopeptide-bound C-terminal SH2 domain of phospholipase C-γ1 (PLCC·pY) have been performed to aid in the interpretation of chem. shift data and the elucidation of interat. interactions at the phosphotyrosine (pTyr) binding region. The simulation of the phosphopeptide complex was carried out with newly developed CHARMM force-field parameters for pTyr, optimized against exptl. data and ab initio calcns. The lack of NOEs involving phosphate in the binding pocket had necessitated a chem. shift anal. of the pTyr binding region for a more detailed characterization of the hydrogen bonding interactions involving pTyr. Although most of these interactions are not present in the NMR structure used as the simulation starting point, the system converges early in the simulation to a structure more compatible with the chem. shift data. This is supported by ab initio detn. of the 1Hη and 1Hε chem. shifts of the three arginines (Arg 18, 37, and 39) in the pTyr binding pocket based on the PLCC· pY MD structure, which are in accord with the exptl. values. The simulation structure of the PLCC·pY complex reveals a more complete picture of interat. interactions in the pTyr binding pocket than is possible with current chem. shift and NOE approaches alone, thereby permitting the identification of the primary pTyr-recognition residues. This pattern of interactions is strikingly similar to those of crystal structures of related SH2 domains. The simulations also suggest several alternative interpretations of the chem. shift data to those suggested in the exptl. investigation (Pascal, S. M., et al. Biochem. 1995, 34, 11353). This insight is valuable as the obsd. chem. shifts could result from a no. of possible pictures of interactions. The present study demonstrates that the combination of mol. dynamics simulations and ab initio chem. shift calcns. can enhance the hydrogen-bonding, amino-arom., and aliph.-arom. information content of NOE- and chem.-shift-based protein structures and serve as a complementary tool for the interpretation of chem. shift data at the at. level.
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    Gargaro, A. R.; Frenkiel, T. A.; Nieto, P. M.; Birdsall, B.; Polshakov, V. I.; Morgan, W. D.; Feeney, J. NMR Detection of arginine-ligand interactions in complexes of lactobacillus casei dihydrofolate reductase. Eur. J. Biochem. 1996, 238, 435– 439,  DOI: 10.1111/j.1432-1033.1996.0435z.x
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    NMR detection of arginine-ligand interactions in complexes of Lactobacillus casei dihydrofolate reductase
    Gargaro, Angelo R.; Frenkiel, Thomas A.; Nieto, Pedro M.; Birdsall, Berry; Polshakov, Vladimir I.; Morgan, William D.; Feeney, James
    European Journal of Biochemistry (1996), 238 (2), 435-439CODEN: EJBCAI; ISSN:0014-2956. (Springer)
    1H-NMR and 15N-NMR signal assignments have been made for the eight arginine residues in Lactobacillus casei dihydrofolate reductase in its binary complex with methotrexate and in its ternary complex with methotrexate and NADPH. 1H-NMR chem. shifts for the guanidino groups of two of the arginines (Arg57 and Arg43) were sensitive to different modes of binding of the guanidino groups with charged oxygen atoms of the ligands. In the complexes formed with methotrexate, Arg57 showed four nonequivalent NHη proton signals indicating hindered rotation about the Nε-Cζ and Cζ-Nη bonds. The NHη12 and NHη22 protons showed large downfield shifts, which would be expected for a sym. end-on interaction of these protons with the charged oxygen atoms of a carboxylate group in methotrexate. These effects were not obsd. for the complex formed with trimethoprim, which does not contain any carboxylate groups. In the complex formed with NADPH present, Arg43 showed a large downfield chem. shift for its NHε proton and a retardation of its rate of exchange with water. This pattern of deshielding contrasts with that detected for Arg57 and is that expected for a side-on interaction of the guanidino group protons with charged oxygen atoms of the ribose 2'-phosphate group of NADPH.
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    Nieto, P. M.; Birdsall, B.; Morgan, W. D.; Frenkiel, T. A.; Gargaro, A. R.; Feeney, J. Correlated bond rotations in interactions of arginine residues with ligand carboxylate groups in protein ligand complexes. FEBS Lett. 1997, 405, 16– 20,  DOI: 10.1016/s0014-5793(97)00147-6
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    Correlated bond rotations in interactions of arginine residues with ligand carboxylate groups in protein ligand complexes
    Nieto, Pedro M.; Birdsall, Berry; Morgan, William D.; Frenkiel, Thomas A.; Gargaro, Angelo R.; Feeney, James
    FEBS Letters (1997), 405 (1), 16-20CODEN: FEBLAL; ISSN:0014-5793. (Elsevier)
    The 1H/15N HSQC NMR spectra of complexes of Lactobacillus casei dihydrofolate reductase contg. methotrexate recorded at 1°C show four resolved signals for the four NHη protons of the Arg57 residue. This is consistent with hindered rotation in the guanidino group resulting from interactions with the α-carboxylate of methotrexate. Increasing the temp. causes exchange line-broadening and coalescence of signals. Rotation rates for the NεCζ and CζNη bonds have been calcd. from lineshape anal. and from zz-HSQC exchange expts. The interactions between the methotrexate α-carboxylate group and the Arg57 guanidino group decrease the rotation rates for the NεCζ bond by about a factor of 10 and those for the CζNη bonds by more than a factor of 100 with respect to their values in free arginine. Furthermore, the relative rates of rotation about these two bonds are reversed in the protein complexes compared with their values in free arginine indicating that there are concerted rotations about the NεCζ bond of the Arg57 guanidino group and the C'Cα bond of the glutamate α-carboxylate group of methotrexate.
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    Morgan, W. D.; Birdsall, B.; Nieto, P. M.; Gargaro, A. R.; Feeney, J. 1H/15N HSQC NMR Studies of Ligand Carboxylate Group Interactions with Arginine Residues in Complexes of Brodimoprim Analogues andLactobacilluscaseiDihydrofolate Reductase. Biochemistry 1999, 38, 2127– 2134,  DOI: 10.1021/bi982359u
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    1H/15N HSQC NMR Studies of Ligand Carboxylate Group Interactions with Arginine Residues in Complexes of Brodimoprim Analogs and Lactobacillus casei Dihydrofolate Reductase
    Morgan, William D.; Birdsall, Berry; Nieto, Pedro M.; Gargaro, Angelo R.; Feeney, James
    Biochemistry (1999), 38 (7), 2127-2134CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)
    1H and 15N NMR studies have been undertaken on complexes of Lactobacillus casei dihydrofolate reductase (DHFR) formed with analogs of the antibacterial drug brodimoprim (2,4-diamino-5-(3',5'-dimethoxy-4'-bromobenzyl)pyrimidine) in order to monitor interactions between carboxylate groups on the ligands and basic residues in the protein. These analogs had been designed by computer modeling with carboxylated alkyl chains introduced at the 3'-O position in order to improve their binding properties by making addnl. interactions with basic groups in the protein. Specific interactions between ligand carboxylate groups and the conserved Arg57 residue have been detected in studies of 1H/15N HSQC spectra of complexes of DHFR with both the 4-carboxylate and the 4,6-dicarboxylate brodimoprim analogs. The spectra from both complexes showed four resolved signals for the four NHη protons of the guanidino group of Arg57, and this is consistent with hindered rotation in the guanidino group resulting from interactions with the 4-carboxylate group in each analog. In the spectra of each complex, one of the protons from each of the two NH2 groups and both nitrogens are considerably deshielded compared to the shielding values normally obsd. for such nuclei. This pattern of deshielding is that expected for a sym. end-on interaction of the carboxylate oxygens with the NHη12 and NHη22 guanidino protons. The differences in the degree of deshielding between the complexes of the two structurally similar brodimoprim analogs and the methotrexate indicates that the shielding is very sensitive to geometry, most probably to hydrogen bond lengths. The 1H/15N HSQC spectrum of the DHFR complex with the brodimoprim-6-carboxylate analog does not feature any deshielded Arg NHη protons and this argues against a similar interaction with the Arg57 in this case. It has not proved possible to det. whether the 6-carboxylate in this analog is interacting directly with any residue in the protein. 1H/15N HSQC spectra have been fully assigned for the complexes with the three brodimoprim analogs and chem. shift mapping used to explore interactions in the binding site. The 1H signals of the bound ligands for all three brodimoprim analogs have been assigned. Their 1H chem. shifts were found to be fairly similar in the different complexes indicating that the 2,4-diaminopyrimidine and the benzyl ring are binding in essentially the same binding sites and with the same overall conformation in the different complexes. The rotation rate about the NεCζ bond in the brodimoprim-4,6-dicarboxylate complex with DHFR has been detd. from a zz-HSQC exchange expt., and its value is quite similar to that obsd. in the DHFR·methotrexate complex (24±10 s-1 at 8° and 50±10 s-1 at 15°, resp.). The 1H and 15N chem. shift differences of selected amide and guanidino NH groups, measured between the DHFR complexes, provided further evidence about the interactions involving Arg57 with the 4-carboxylate and 4,6-dicarboxylate brodimoprim analogs.
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  1. Giovanni Montà-González, Félix Sancenón, Ramón Martínez-Máñez, Vicente Martí-Centelles. Purely Covalent Molecular Cages and Containers for Guest Encapsulation. Chemical Reviews 2022, 122 (16) , 13636-13708. https://doi.org/10.1021/acs.chemrev.2c00198
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  • Abstract

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    Figure 1

    Figure 1. Illustration of the selected guests (L/S red and D/R blue).

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    Figure 2

    Figure 2. Illustration of the three selected signals of CC3-R.

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    Figure 3

    Figure 3. 1H NMR data for H2 signal of the host with both enantiomers of ligand 1 at several concentrations.

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    Figure 4

    Figure 4. 1H NMR region for the corresponding methyl group signal of ligand 1 at 3 mM and the host at 2.5 mM; (a) rac-1; (b) S-1; (c) R-1; and (d) isolated S-1.

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    Figure 5

    Figure 5. DFT structures for the interaction CC3-R–guest; l-1 and d-1; l-2 and d-2.

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      10
      Multi-scale crystal engineering of metal organic frameworks
      Seoane, Beatriz; Castellanos, Sonia; Dikhtiarenko, Alla; Kapteijn, Freek; Gascon, Jorge
      Coordination Chemistry Reviews (2016), 307 (Part_2), 147-187CODEN: CCHRAM; ISSN:0010-8545. (Elsevier B.V.)
      A review. During the last decade the no. of publications related to the synthesis of new metal-org. frameworks or coordination polymers has grown almost exponentially. Many of them are devoted to the study of the correlation between the mol. components (linkers and metal nodes or clusters) and the final properties of the resulting structure. Withal, the field of metal-org. frameworks has also witnessed important advances in the development of synthetic tools to control the particle size and shape and to obtain secondary porosity by applying knowledge from three disciplines: crystallog., coordination chem. and chem. engineering. These tools allow for crystal engineering beyond the mol. scale extending over the meso and macro scales, so that certain degree of multi-scale design is already possible. In this manner, MOFs' performance were improved in certain applications by choosing the optimal particle morphol. and dimensions that enhance the materials' properties and/or facilitate their implementation on functional devices. This review highlights the latest advances on MOF crystal engineering, with special emphasis on the meso and macro scales. After discussing some general considerations on the fundamentals of MOF crystn., the authors examine different synthetic approaches developed to tune the MOF particle size, shape and textural properties and the impact this multi-scale MOF crystal engineering showed so far in different applications. Finally, the authors' view on possible future research directions is outlined.
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    11. 11
      Chen, L.; Luque, R.; Li, Y. Controllable design of tunable nanostructures inside metal-organic frameworks. Chem. Soc. Rev. 2017, 46, 4614– 4630,  DOI: 10.1039/c6cs00537c
      11
      Controllable design of tunable nanostructures inside metal-organic frameworks
      Chen, Liyu; Luque, Rafael; Li, Yingwei
      Chemical Society Reviews (2017), 46 (15), 4614-4630CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)
      The controllable encapsulation of nanoentities (such as metal nanoparticles, quantum dots, polyoxometalates, org. and metallorg. mols., biomacromols., and metal-org. polyhedra) into metal-org. frameworks (MOFs) to form composite materials has attracted significant research interest in a variety of fields. These composite materials not only exhibit the properties of both the nanoentities and the MOFs but also display unique and synergistic functionalities. Tuning the sizes, compns., and shapes of nanoentities encapsulated in MOFs enables the final composites to exhibit superior performance to those of the sep. constituents for various applications. In this tutorial review article, we summarized the state-of-the-art development of MOFs contg. encapsulated tunable nanoentities, with special emphasis on the prepn. and synergistic properties of these composites.
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    12. 12
      Zhang, Y.-B.; Su, J.; Furukawa, H.; Yun, Y.; Gándara, F.; Duong, A.; Zou, X.; Yaghi, O. M. Single-crystal structure of a covalent organic framework. J. Am. Chem. Soc. 2013, 135, 16336– 16339,  DOI: 10.1021/ja409033p
      12
      Single-Crystal Structure of a Covalent Organic Framework
      Zhang, Yue-Biao; Su, Jie; Furukawa, Hiroyasu; Yun, Yifeng; Gandara, Felipe; Duong, Adam; Zou, Xiaodong; Yaghi, Omar M.
      Journal of the American Chemical Society (2013), 135 (44), 16336-16339CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      The crystal structure of a new covalent org. framework, termed COF-320, is detd. by single-crystal 3D electron diffraction using the rotation electron diffraction (RED) method for data collection. The COF crystals are prepd. by an imine condensation of tetra-(4-anilyl)-methane and 4,4'-biphenyldialdehyde in 1,4-dioxane at 120 °C to produce a highly porous 9-fold interwoven diamond net. COF-320 exhibits permanent porosity with a Langmuir surface area of 2400 m2/g and a methane total uptake of 15.0 wt. % (176 cm3/cm3) at 25 °C and 80 bar. The successful detn. of the structure of COF-320 directly from single-crystal samples is an important advance in the development of COF chem.
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    13. 13
      Díaz, U.; Corma, A. Ordered covalent organic frameworks, COFs and PAFs. From preparation to application. Coord. Chem. Rev. 2016, 311, 85– 124,  DOI: 10.1016/j.ccr.2015.12.010
      13
      Ordered covalent organic frameworks, COFs and PAFs. From preparation to application
      Diaz, Urbano; Corma, Avelino
      Coordination Chemistry Reviews (2016), 311 (), 85-124CODEN: CCHRAM; ISSN:0010-8545. (Elsevier B.V.)
      Covalent org. frameworks, COFs, and their derived sub-groups based on auto-assembly of exclusively arom. units, PAFs, are emerging into the advanced materials field due to their high free porous vol., structural regularity, robustness, hydrothermal stability, and functional variety. They present high gas uptake capacities and presence of stabilized active functions in the framework. This together with charged low-d. structures combined with their organization through π-conjugated system arrays, open the possibilities of COFs and PAFs to be used as effective materials for adsorption, selective sepn. and catalysis, and in nanotechnol. applications. This review will be focused on self-assembly synthesis mechanisms, physico-chem. characteristics, and applications of this class of promising covalent porous org. structures, out looking their possible future approaches and perspectives.
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    14. 14
      Das, S.; Heasman, P.; Ben, T.; Qiu, S. Porous Organic Materials: Strategic Design and Structure-Function Correlation. Chem. Rev. 2017, 117, 1515– 1563,  DOI: 10.1021/acs.chemrev.6b00439
      14
      Porous organic material strategic design and structure-function correlation
      Das, Saikat; Heasman, Patrick; Ben, Teng; Qiu, Shilun
      Chemical Reviews (Washington, DC, United States) (2017), 117 (3), 1515-1563CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)
      Porous org. materials have garnered colossal interest with the scientific fraternity due to their excellent gas sorption performances, catalytic abilities, energy storage capacities, and other intriguing applications. This review encompasses the recent significant breakthroughs and the conventional functions and practices in the field of porous org. materials to find useful applications and imparts a comprehensive understanding of the strategic evolution of the design and synthetic approaches of porous org. materials with tunable characteristics. We present an exhaustive anal. of the design strategies with special emphasis on the topologies of cryst. and amorphous porous org. materials. In addn. to elucidating the structure-function correlation and state-of-the-art applications of porous org. materials, we address the challenges and restrictions that prevent us from realizing porous org. materials with tailored structures and properties for useful applications.
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    15. 15
      Dawson, R.; Cooper, A. I.; Adams, D. J. Nanoporous organic polymer networks. Prog. Polym. Sci. 2012, 37, 530– 563,  DOI: 10.1016/j.progpolymsci.2011.09.002
      15
      Nanoporous organic polymer networks
      Dawson, Robert; Cooper, Andrew I.; Adams, Dave J.
      Progress in Polymer Science (2012), 37 (4), 530-563CODEN: PRPSB8; ISSN:0079-6700. (Elsevier Ltd.)
      A review. Nanoporous org. polymer networks are a class of materials consisting solely of the lighter elements in the periodic table. These materials have potential uses in areas such as storage, sepn., and catalysis. Here, we review the different classes of nanoporous polymer networks including covalent org. frameworks, hypercrosslinked polymers, conjugated microporous polymers, and polymers of intrinsic microporosity. The growing variety in synthetic routes to these materials allows a range of different polymer networks to be formed, including cryst. and amorphous structures. It is also possible to incorporate many different kinds of functional groups in a modular fashion. So far, most networks have been examd. from the perspective of gas sorption, and this area is discussed critically and in depth in this review. The use of nanoporous org. polymers for applications such as catalysis and sepns. is an important developing area, and we discuss recent developments as well as highlighting potential future opportunities.
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    16. 16
      Tan, L.; Tan, B. Hypercrosslinked porous polymer materials: design, synthesis, and applications. Chem. Soc. Rev. 2017, 46, 3322– 3356,  DOI: 10.1039/c6cs00851h
      16
      Hypercrosslinked porous polymer materials: design, synthesis, and applications
      Tan, Liangxiao; Tan, Bien
      Chemical Society Reviews (2017), 46 (11), 3322-3356CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)
      A review. Hypercrosslinked polymers (HCPs) are a series of permanent microporous polymer materials initially reported by Davankov, and have received an increasing level of research interest. In recent years, HCPs have experienced rapid growth due to their remarkable advantages such as diverse synthetic methods, easy functionalization, high surface area, low cost reagents and mild operating conditions. Judicious selection of monomers, appropriate length crosslinkers and optimized reaction conditions yielded a well-developed polymer framework with an adjusted porous topol. Post fabrication of the as developed network facilitates the incorporation of various chem. functionalities that may lead to interesting properties and enhance the selection toward a specific application. To date, numerous HCPs have been prepd. by post-crosslinking polystyrene-based precursors, one-step self-polycondensation or external crosslinking strategies. The advent of these methodologies has prompted researchers to construct well-defined porous polymer networks with customized micromorphol. and functionalities. In this review, we describe not only the basic synthetic principles and strategies of HCPs, but also the advancements in the structural and morphol. study as well as the frontiers of potential applications in energy and environmental fields such as gas storage, carbon capture, removal of pollutants, mol. sepn., catalysis, drug delivery, sensing, etc.
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    17. 17
      Bojdys, M. J.; Hasell, T.; Severin, N.; Jelfs, K. E.; Rabe, J. P.; Cooper, A. I. Porous organic cage crystals: characterising the porous crystal surface. Chem. Commun. 2012, 48, 11948– 11950,  DOI: 10.1039/c2cc36602a
      17
      Porous organic cage crystals: characterizing the porous crystal surface
      Bojdys, Michael J.; Hasell, Tom; Severin, Nikolai; Jelfs, Kim E.; Rabe, Juergen P.; Cooper, Andrew I.
      Chemical Communications (Cambridge, United Kingdom) (2012), 48 (98), 11948-11950CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)
      The characterization of porous cryst. solids often relies on single crystal x-ray diffraction, which does not give direct information about the surface of the material. Here, crystals of a porous org. cage, CC3-R, were studied by at. force microscopy and shown to possess two distinct gas-solid interfaces, proving that the bulk crystal structure is preserved at the porous crystal surface.
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    18. 18
      Tozawa, T.; Jones, J. T. A.; Swamy, S. I.; Jiang, S.; Adams, D. J.; Shakespeare, S.; Clowes, R.; Bradshaw, D.; Hasell, T.; Chong, S. Y.; Tang, C.; Thompson, S.; Parker, J.; Trewin, A.; Bacsa, J.; Slawin, A. M. Z.; Steiner, A.; Cooper, A. I. Porous organic cages. Nat. Mater. 2009, 8, 973– 978,  DOI: 10.1038/nmat2545
      18
      Porous organic cages
      Tozawa, Tomokazu; Jones, James T. A.; Swamy, Shashikala I.; Jiang, Shan; Adams, Dave J.; Shakespeare, Stephen; Clowes, Rob; Bradshaw, Darren; Hasell, Tom; Chong, Samantha Y.; Tang, Chiu; Thompson, Stephen; Parker, Julia; Trewin, Abbie; Bacsa, John; Slawin, Alexandra M. Z.; Steiner, Alexander; Cooper, Andrew I.
      Nature Materials (2009), 8 (12), 973-978CODEN: NMAACR; ISSN:1476-1122. (Nature Publishing Group)
      Porous materials are important in a wide range of applications including mol. sepns. and catalysis. Covalently bonded org. cages can assemble into cryst. microporous materials. The porosity is prefabricated and intrinsic to the mol. cage structure, as opposed to being formed by noncovalent self-assembly of nonporous sub-units. The three-dimensional connectivity between the cage windows is controlled by varying the chem. functionality such that either nonporous or permanently porous assemblies can be produced. Surface areas and gas uptakes for the latter exceed comparable mol. solids. One of the cages can be converted by recrystn. to produce either porous or nonporous polymorphs with apparent Brunauer-Emmett-Teller surface areas of 550 and 23 m2 g-1, resp. These results suggest design principles for responsive porous org. solids and for the modular construction of extended materials from prefabricated mol. pores.
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    19. 19
      Chen, L.; Reiss, P. S.; Chong, S. Y.; Holden, D.; Jelfs, K. E.; Hasell, T.; Little, M. A.; Kewley, A.; Briggs, M. E.; Stephenson, A.; Thomas, K. M.; Armstrong, J. A.; Bell, J.; Busto, J.; Noel, R.; Liu, J.; Strachan, D. M.; Thallapally, P. K.; Cooper, A. I. Separation of rare gases and chiral molecules by selective binding in porous organic cages. Nat. Mater. 2014, 13, 954– 960,  DOI: 10.1038/nmat4035
      19
      Separation of rare gases and chiral molecules by selective binding in porous organic cages
      Chen, Linjiang; Reiss, Paul S.; Chong, Samantha Y.; Holden, Daniel; Jelfs, Kim E.; Hasell, Tom; Little, Marc A.; Kewley, Adam; Briggs, Michael E.; Stephenson, Andrew; Thomas, K. Mark; Armstrong, Jayne A.; Bell, Jon; Busto, Jose; Noel, Raymond; Liu, Jian; Strachan, Denis M.; Thallapally, Praveen K.; Cooper, Andrew I.
      Nature Materials (2014), 13 (10), 954-960CODEN: NMAACR; ISSN:1476-1122. (Nature Publishing Group)
      A porous org. cage mol. having unprecedented performance in the solid state for the sepn. of rare gases, such as krypton and xenon, is reported. The selectivity arises from a precise size match between the rare gas and the org. cage cavity, as predicted by mol. simulations. Breakthrough expts. demonstrate real practical potential for the sepn. of krypton, xenon and radon from air at concns. of only a few ppm. Selective binding of chiral org. mols. such as 1-phenylethanol is also demonstrated, suggesting applications in enantioselective sepn.
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    20. 20
      Briggs, M. E.; Slater, A. G.; Lunt, N.; Jiang, S.; Little, M. A.; Greenaway, R. L.; Hasell, T.; Battilocchio, C.; Ley, S. V.; Cooper, A. I. Dynamic flow synthesis of porous organic cages. Chem. Commun. 2015, 51, 17390– 17393,  DOI: 10.1039/c5cc07447a
      20
      Dynamic flow synthesis of porous organic cages
      Briggs, Michael E.; Slater, Anna G.; Lunt, Neil; Jiang, Shan; Little, Marc A.; Greenaway, Rebecca L.; Hasell, Tom; Battilocchio, Claudio; Ley, Steven V.; Cooper, Andrew I.
      Chemical Communications (Cambridge, United Kingdom) (2015), 51 (98), 17390-17393CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)
      The dynamic covalent synthesis of two imine-based porous org. cages was successfully transferred from batch to continuous flow. The same flow reactor was then used to scramble the constituents of these two cages in differing ratios to form cage mixts. Preparative HPLC purifn. of one of these mixts. allowed rapid access to a desymmetrised cage mol.
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    21. 21
      Jiang, S.; Jones, J. T. A.; Hasell, T.; Blythe, C. E.; Adams, D. J.; Trewin, A.; Cooper, A. I. Porous organic molecular solids by dynamic covalent scrambling. Nat. Commun. 2011, 2, 207,  DOI: 10.1038/ncomms1207
      21
      Porous organic molecular solids by dynamic covalent scrambling
      Jiang Shan; Jones James T A; Hasell Tom; Blythe Charlotte E; Adams Dave J; Trewin Abbie; Cooper Andrew I
      Nature communications (2011), 2 (), 207 ISSN:.
      The main strategy for constructing porous solids from discrete organic molecules is crystal engineering, which involves forming regular crystalline arrays. Here, we present a chemical approach for desymmetrizing organic cages by dynamic covalent scrambling reactions. This leads to molecules with a distribution of shapes which cannot pack effectively and, hence, do not crystallize, creating porosity in the amorphous solid. The porous properties can be fine tuned by varying the ratio of reagents in the scrambling reaction, and this allows the preparation of materials with high gas selectivities. The molecular engineering of porous amorphous solids complements crystal engineering strategies and may have advantages in some applications, for example, in the compatibilization of functionalities that do not readily cocrystallize.
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    22. 22
      Little, M. A.; Chong, S. Y.; Schmidtmann, M.; Hasell, T.; Cooper, A. I. Guest control of structure in porous organic cages. Chem. Commun. 2014, 50, 9465– 9468,  DOI: 10.1039/c4cc04158e
      22
      Guest control of structure in porous organic cages
      Little, Marc A.; Chong, Samantha Y.; Schmidtmann, Marc; Hasell, Tom; Cooper, Andrew I.
      Chemical Communications (Cambridge, United Kingdom) (2014), 50 (67), 9465-9468CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)
      Two porous org. cages with different thermodn. polymorphs were induced by co-solvents to interchange their crystal packing modes, thus achieving guest-mediated control over solid-state porosity. In situ crystallog. allows the effect of the co-solvent guests on these structural interconversions to be understood.
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    23. 23
      Kewley, A.; Stephenson, A.; Chen, L.; Briggs, M. E.; Hasell, T.; Cooper, A. I. Porous organic cages for gas chromatography separations. Chem. Mater. 2015, 27, 3207– 3210,  DOI: 10.1021/acs.chemmater.5b01112
      23
      Porous Organic Cages for Gas Chromatography Separations
      Kewley, Adam; Stephenson, Andrew; Chen, Linjiang; Briggs, Michael E.; Hasell, Tom; Cooper, Andrew I.
      Chemistry of Materials (2015), 27 (9), 3207-3210CODEN: CMATEX; ISSN:0897-4756. (American Chemical Society)
      Chromatog. is an important process for characterizing and purifying org. mols., but some mixts. remain challenging to sep. The authors report the 1st use of a soln.-processable porous org. cage mol., (I, CC3), as a stationary phase for gas chromatog. Capillary columns were coated with CC3 using a simple, static coating method. These columns are versatile and can sep. alkanes, arom. mixts., and chiral mols. Atomistic simulations indicate that the efficient shape sorting of branched hexane isomers by CC3 results from a combination of kinetic diffusion and surface-interaction effects.
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    24. 24
      Briggs, M. E.; Cooper, A. I. A perspective on the synthesis, purification, and characterization of porous organic cages. Chem. Mater. 2017, 29, 149– 157,  DOI: 10.1021/acs.chemmater.6b02903
      24
      A Perspective on the Synthesis, Purification, and Characterization of Porous Organic Cages
      Briggs, Michael E.; Cooper, Andrew I.
      Chemistry of Materials (2017), 29 (1), 149-157CODEN: CMATEX; ISSN:0897-4756. (American Chemical Society)
      A review with authors data. Porous org. cages present many opportunities in functional materials chem., but the synthetic challenges for these mol. solids are somewhat different from those faced in the areas of metal-org. frameworks, covalent-org. frameworks, or porous polymer networks. Here, we highlight the practical methods that we have developed for the design, synthesis, and characterization of imine porous org. cages using CC1 and CC3 as examples. The key points are transferable to other cages, and this perspective should serve as a practical guide to researchers who are new to this field.
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    25. 25
      Xie, S.-M.; Zhang, J.-H.; Fu, N.; Wang, B.-J.; Chen, L.; Yuan, L.-M. A chiral porous organic cage for molecular recognition using gas chromatography. Anal. Chim. Acta 2016, 903, 156– 163,  DOI: 10.1016/j.aca.2015.11.030
      25
      A chiral porous organic cage for molecular recognition using gas chromatography
      Xie, Sheng-Ming; Zhang, Jun-Hui; Fu, Nan; Wang, Bang-Jin; Chen, Ling; Yuan, Li-Ming
      Analytica Chimica Acta (2016), 903 (), 156-163CODEN: ACACAM; ISSN:0003-2670. (Elsevier B.V.)
      Mol. org. cages as shape-persistent org. mols. with permanent and accessible cavities have attracted a lot of interest because of their importance as host-guest systems. Herein, the authors report a chiral porous org. cage (POC) CC9 dild. with a polysiloxane OV-1701 to fabricate a CC9-coated capillary column, which was used for the high-resoln. gas chromatog. sepn. of org. compds., including positional isomers and racemates. On the porous org. cage CC9-coated capillary column, a large no. of racemic compds. such as chiral alcs., esters, ethers and epoxides can be resolved without derivatization. By comparing the chiral recognition ability of the CC9-coated column with the com. available β-DEX 120 column and the POC CC3-R coated column recently reported by the authors' group, the CC9-coated column offered good resoln. during the sepn. of some racemates, that were not sepd. using the β-DEX 120 column or POC CC3-R coated column. Therefore, the CC9-coated column can be complementary to the β-DEX 120 column and CC3-R coated column. The CC9-coated column exhibited great potential for application in the sepn. of positional isomers and enantiomers with great selectivity, high resoln. and good reproducibility.
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    26. 26
      Zhang, J.-H.; Xie, S.-M.; Chen, L.; Wang, B.-J.; He, P.-G.; Yuan, L.-M. Homochiral porous organic cage with high selectivity for the separation of racemates in gas chromatography. Anal. Chem. 2015, 87, 7817– 7824,  DOI: 10.1021/acs.analchem.5b01512
      26
      Homochiral Porous Organic Cage with High Selectivity for the Separation of Racemates in Gas Chromatography
      Zhang, Jun-Hui; Xie, Sheng-Ming; Chen, Ling; Wang, Bang-Jin; He, Pin-Gang; Yuan, Li-Ming
      Analytical Chemistry (Washington, DC, United States) (2015), 87 (15), 7817-7824CODEN: ANCHAM; ISSN:0003-2700. (American Chemical Society)
      Porous org. mol. cages as a new type of porous materials have attracted a tremendous attention for their potential applications in recent years. Here the authors report the use of a homochiral porous org. cage (POC) (CC3-R) dild. with a polysiloxane (OV-1701) as a stationary phase for high-resoln. gas chromatog. (GC) with excellent enantioselectivity. A large no. of optical isomers were resolved without derivatization, including chiral alcs., diols, amines, alc. amines, esters, ketones, ethers, halohydrocarbons, org. acids, amino acid Me esters, and sulfoxides. Compared with com. β-DEX 120 and Chirasil-L-Val columns, the CC3-R coated capillary column offered more preeminent enantioselectivity. CC3-R also exhibits good selectivity for the sepn. of isomers, linear alkanes, alcs., and arom. hydrocarbons. The excellent resoln. ability, repeatability, and thermal stability make CC3-R a promising candidate as a novel stationary phase for GC. The study described herein first proves useful com. Also porous org. mol. materials will become more attractive in sepn. science.
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    27. 27
      Stilbs, P. Fourier transform pulsed-gradient spin-echo studies of molecular diffusion. Prog. Nucl. Magn. Reson. Spectrosc. 1987, 19, 1– 45,  DOI: 10.1016/0079-6565(87)80007-9
      27
      Fourier transform pulsed-gradient spin-echo studies of molecular diffusion
      Stilbs, Peter
      Progress in Nuclear Magnetic Resonance Spectroscopy (1987), 19 (1), 1-45CODEN: PNMRAT; ISSN:0079-6565.
      A review with 193 refs. is given on NMR methods (esp. Fourier-transform, pulsed-field-gradient, spin-echo NMR) in measuring mol. diffusion (self-diffusion, mutual diffusion, and multicomponent diffusion) in various types of systems (including liqs., liq. mixts., polymer and polyelectrolyte solns., gels, surfactant aq. solns., and emulsions).
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    28. 28
      Tyrrell, H. J. V.; Harris, R. K. Diffusion in Liquids; Butterworths: London, 1984.
      There is no corresponding record for this reference.
    29. 29
      Zhao, Y.; Truhlar, D. G. The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals. Theor. Chem. Acc. 2008, 120, 215– 241,  DOI: 10.1007/s00214-007-0310-x
      29
      The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals
      Zhao, Yan; Truhlar, Donald G.
      Theoretical Chemistry Accounts (2008), 120 (1-3), 215-241CODEN: TCACFW; ISSN:1432-881X. (Springer GmbH)
      We present two new hybrid meta exchange-correlation functionals, called M06 and M06-2X. The M06 functional is parametrized including both transition metals and nonmetals, whereas the M06-2X functional is a high-nonlocality functional with double the amt. of nonlocal exchange (2X), and it is parametrized only for nonmetals. The functionals, along with the previously published M06-L local functional and the M06-HF full-Hartree-Fock functionals, constitute the M06 suite of complementary functionals. We assess these four functionals by comparing their performance to that of 12 other functionals and Hartree-Fock theory for 403 energetic data in 29 diverse databases, including ten databases for thermochem., four databases for kinetics, eight databases for noncovalent interactions, three databases for transition metal bonding, one database for metal atom excitation energies, and three databases for mol. excitation energies. We also illustrate the performance of these 17 methods for three databases contg. 40 bond lengths and for databases contg. 38 vibrational frequencies and 15 vibrational zero point energies. We recommend the M06-2X functional for applications involving main-group thermochem., kinetics, noncovalent interactions, and electronic excitation energies to valence and Rydberg states. We recommend the M06 functional for application in organometallic and inorganometallic chem. and for noncovalent interactions.
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    30. 30
      Krishnan, R.; Binkley, J. S.; Seeger, R.; Pople, J. A. Self-consistent molecular orbital methods. XX. A basis set for correlated wave functions. J. Chem. Phys. 1980, 72, 650– 654,  DOI: 10.1063/1.438955
      30
      Self-consistent molecular orbital methods. XX. A basis set for correlated wave functions
      Krishnan, R.; Binkley, J. S.; Seeger, R.; Pople, J. A.
      Journal of Chemical Physics (1980), 72 (1), 650-4CODEN: JCPSA6; ISSN:0021-9606.
      A contracted Gaussian basis set (6-311G**) is developed by optimizing exponents and coeffs. at the Moller-Plesset (MP) second-order level for the ground states of first-row atoms. This has a triple split in the valence s and p shells together with a single set of uncontracted polarization functions on each atom. The basis is tested by computing structures and energies for some simple mols. at various levels of MP theory and comparing with expt.
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    31. 31
      Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Petersson, G. A.; Nakatsuji, H.; Gaussian 09, Revision C.01; Gaussian, Inc.: Wallingford CT, 2009.
      There is no corresponding record for this reference.
    32. 32
      Stejskal, E. O.; Tanner, J. E. Spin Diffusion Measurements: Spin Echoes in the Presence of a Time-Dependent Field Gradient. J. Chem. Phys. 1965, 42, 288– 292,  DOI: 10.1063/1.1695690
      32
      Spin diffusion measurements: spin echoes in the presence of a time-dependent field gradient
      Stejskal, E. O.; Tanner, J. E.
      Journal of Chemical Physics (1965), 42 (1), 288-92CODEN: JCPSA6; ISSN:0021-9606.
      A derivation is given of the effect of a time-dependent magnetic field gradient on the spin-echo expt., particularly in the presence of spin diffusion. There are several reasons for preferring certain kinds of time-dependent magnetic field gradients to the more usual steady gradient. If the gradient is reduced during the radio-frequency pulses, H1 need not be particularly large; if the gradient is small at the time of the echo, the echo will be broad and its amplitude easy to measure. Both of these relaxations of restrictions on the measurement of diffusion coeffs. by the spin-echo technique serve to extend its range of applicability. A pulsed gradient can be recommended when it is crit. to define the precise time period over which diffusion is being measured. The theoretical expression derived was verified exptl. for several choices of time-dependent magnetic field gradient. An app. is described suitable for the production of pulsed gradients with amplitudes as large as 100 gauss cm. The diffusion coeff. of dry glycerol at 26° ± 1° is (2.5 ± 0.2) × 10-3 cm.2/sec., a value smaller than can ordinarily be measured by the steady gradient method.
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    33. 33
      Tanner, J. E. Use of the stimulated echo in NMR diffusion studies. J. Chem. Phys. 1970, 52, 2523– 2526,  DOI: 10.1063/1.1673336
      33
      Use of the stimulated echo in NMR diffusion studies
      Tanner, John E.
      Journal of Chemical Physics (1970), 52 (5), 2523-6CODEN: JCPSA6; ISSN:0021-9606.
      The stimulated echo in a three-radio-frequency-pulse expt. is useful in extending the range of measurement of diffusion coeffs. to more viscous substances or the measurement of barrier sepns. to wider spacings in systems where the diffusing substance has T1 > T2. The spin-echo attenuation due to self-diffusion is derived for the general case of a time-dependent field gradient, and the result is found exptl. to be correct for the special case of a field gradient applied in 2 equal, square pulse.
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    34. 34
      Johnson, C. S. Diffusion ordered nuclear magnetic resonance spectroscopy: principles and applications. Magn. Reson. Spectrosc. 1999, 34, 203– 256,  DOI: 10.1016/s0079-6565(99)00003-5
      34
      Diffusion ordered nuclear magnetic resonance spectroscopy: principles and applications
      Johnson, C. S., Jr.
      Progress in Nuclear Magnetic Resonance Spectroscopy (1999), 34 (3,4), 203-256CODEN: PNMRAT; ISSN:0079-6565. (Elsevier Science B.V.)
      A review with 146 refs.
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    35. 35
      Chen, A.; Wu, D.; Johnson, C. S. Determination of molecular weight distributions for polymers by diffusion-ordered NMR. J. Am. Chem. Soc. 1995, 117, 7965– 7970,  DOI: 10.1021/ja00135a015
      35
      Determination of Molecular Weight Distributions for Polymers by Diffusion-Ordered NMR
      Chen, Aidi; Wu, Donghui; Johnson, Charles S., Jr.
      Journal of the American Chemical Society (1995), 117 (30), 7965-70CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      Diffusion-ordered NMR spectroscopy, a technique based on pulsed field gradient NMR (PFGNMR), was used to characterize mol. wt. distributions for samples of poly(ethylene oxide) in D2O. The distribution of diffusion coeffs. G(D) was obtained by anal. of PFGNMR data with a modified version of the well-known constrained regularization program CONTIN. Regularization was considerably improved for broad distributions by setting the wts. cm in CONTIN's quadrature formula equal to (Dm/Dmax)xm, where Dmax is the diffusion coeff. corresponding to the max. in G(Dm)Dm and m is an index. Here xm varies linearly from +2 to -2 with log(Dm) across the distribution. This amts. to enhancing low amplitude regions of G(D)D during anal. The estd. distribution was then converted to the mass weighted distribution of mol. wts. by means of the relation D = 10-7.62 M-0.62 (with D in units of m2 s-1) obtained from expts. on monodisperse ref. stds. In this study spin relaxation rates were independent of mol. wts. and intermol. averaging effects were insignificant. As an illustration, mol. wt. distributions were detd. for two broadly distributed samples. The no. and wt. av. mol. wts. and the polydispersities agreed well with values provided by the manufacturer when the PFGNMR data sets had signal-to-noise ratios greater than 500.
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    36. 36
      Avram, L.; Cohen, Y. Diffusion NMR of molecular cages and capsules. Chem. Soc. Rev. 2015, 44, 586– 602,  DOI: 10.1039/c4cs00197d
      36
      Diffusion NMR of molecular cages and capsules
      Avram, Liat; Cohen, Yoram
      Chemical Society Reviews (2015), 44 (2), 586-602CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)
      A review. In the last decade diffusion NMR and diffusion ordered spectroscopy (DOSY) have become important anal. tools for the characterization of supramol. systems in soln. Diffusion NMR can be used to glean information on the (effective) size and shape of mol. species, as well as to probe inter-mol. interactions and can be used to est. the assocn. const. (Ka) of a complex. In addn., the diffusion coeff., as obtained from diffusion NMR, is a much more intuitive parameter than the chem. shift for probing self-assocn., aggregation and inter-mol. interactions. The diffusion coeff. may be an even more important anal. parameter in systems in which the formed supramol. entity has the same symmetry as its building units, when there is a large change in the mol. wt., where many mol. species are involved in the formation of the supramol. systems, and when proton transfer may occur which, in turn, may affect the chem. shift. Some of the self-assembled mol. capsules and cages prepd. in the last decade represent such supramol. systems and in the present review, following a short introduction on diffusion NMR, we survey the contribution of diffusion NMR and DOSY in the field of mol. containers and capsules. We will 1st focus on the role played by diffusion NMR in the field of H-bond driven self-assembled capsules. We then survey the contributions of diffusion NMR and DOSY to the study and characterization of metal-ligand cages and capsules. Finally, we describe a few recent applications of diffusion NMR in the field of hydrophobic, electrostatic and covalent containers.
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    37. 37
      Åslund, I.; Nowacka, A.; Nilsson, M.; Topgaard, D. Filter-exchange PGSE NMR determination of cell membrane permeability. J. Magn. Reson. 2009, 200, 291– 295,  DOI: 10.1016/j.jmr.2009.07.015
      37
      Filter-exchange PGSE NMR determination of cell membrane permeability
      Aslund Ingrid; Nowacka Agnieszka; Nilsson Markus; Topgaard Daniel
      Journal of magnetic resonance (San Diego, Calif. : 1997) (2009), 200 (2), 291-5 ISSN:.
      A new PGSE NMR sequence is introduced for measuring diffusive transport across the plasma membrane of living cells. A "diffusion filter" and a variable mixing time precedes a standard PGSE block for diffusion encoding of the NMR signal. The filter is a PGSE block optimized for selectively removing the magnetization of the extracellular water. With increasing mixing time the intra- and extracellular components approach their equilibrium fractional populations. The rate of exchange can be measured using only a few minutes of instrument time. Water exchange over the plasma membrane of starved yeast cells is studied in the temperature range +5 to +32 degrees C.
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    38. 38
      Occhipinti, P.; Griffiths, P. C. Quantifying diffusion in mucosal systems by pulsed-gradient spin-echo NMR. Adv. Drug Delivery Rev. 2008, 60, 1570– 1582,  DOI: 10.1016/j.addr.2008.08.006
      38
      Quantifying diffusion in mucosal systems by pulsed-gradient spin-echo NMR
      Occhipinti, Paola; Griffiths, Peter C.
      Advanced Drug Delivery Reviews (2008), 60 (15), 1570-1582CODEN: ADDREP; ISSN:0169-409X. (Elsevier B.V.)
      A review. Mucus, a thick and slimy secretion produced by submucosal cells, covers many epithelial surfaces in mammalian organs and prevents foreign particles that enter the body from accessing cells. However, the mucus layer also represents a potential barrier to the efficient delivery of nano-sized drug delivery systems (polyplexes, lipoplexes, particles) to the underlying mucosal epithelium. Many studies have considered the ability of nano-sized particles and polymers to diffuse within the mucosal network using a range of different techniques, including multiple-particle tracking (MPT), diffusion chamber studies and fluorescence recovery after photobleaching (FRAP). This review highlights the current understanding of the interaction of the diffusion of nano-sized structures within mucosal networks. Moreover, this article presents an introduction to pulsed-gradient spin-echo NMR (PGSE-NMR), a potential new tool to investigate the mobility of mol. species through mucosal networks and related biol. gels.
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    39. 39
      Marega, R.; Aroulmoji, V.; Dinon, F.; Vaccari, L.; Giordani, S.; Bianco, A.; Murano, E.; Prato, M. Diffusion-ordered NMR spectroscopy in the structural characterization of functionalized carbon nanotubes. J. Am. Chem. Soc. 2009, 131, 9086– 9093,  DOI: 10.1021/ja902728w
      39
      Diffusion-Ordered NMR Spectroscopy in the Structural Characterization of Functionalized Carbon Nanotubes
      Marega, Riccardo; Aroulmoji, Vincent; Dinon, Francesca; Vaccari, Lisa; Giordani, Silvia; Bianco, Alberto; Murano, Erminio; Prato, Maurizio
      Journal of the American Chemical Society (2009), 131 (25), 9086-9093CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      The emerging applications of functionalized C nanotubes (CNTs) in various research domains necessitate the use of many different anal. techniques to confirm their structural modifications in a fast and reliable manner. Thus far, NMR spectroscopy was not among the main tools for characterization of organically modified C nanostructures. 1H anal. is limited because the signals in these derivs. are typically weak and broad, resulting in uncertainties of a few ppm, and because of the strong interference of residual solvent signals. To overcome these limitations, the authors studied the applicability of 1H NMR spectroscopy based on gradient-edited diffusion pulse sequences (1-dimensional diffusion-ordered spectroscopy, DOSY) in the characterization of CNT derivs. In general, diffusion NMR expts. allow the sepn. of NMR signals of different species present in a mixt., according to their own diffusion coeffs., merging spectroscopy information with size anal. A selected set of CNT derivs. was synthesized and analyzed using 1-dimensional DOSY expts. by applying strong magnetic field gradients (up to 42.6 G cm-1). Colorimetric tests (i.e., Kaiser test) and TGA anal. support the NMR findings, which are related to isolated and/or bundled short SWNTs, from TEM and AFM characterization. The overall results show that the diffusion-based NMR spectroscopy is a fast and promising approach for the characterization of covalently modified CNT derivs.
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    40. 40
      Canzi, G.; Mrse, A. A.; Kubiak, C. P. Diffusion-ordered NMR spectroscopy as a reliable alternative to TEM for determining the size of gold nanoparticles in organic solutions. J. Phys. Chem. C 2011, 115, 7972– 7978,  DOI: 10.1021/jp2008557
      40
      Diffusion-Ordered NMR Spectroscopy as a Reliable Alternative to TEM for Determining the Size of Gold Nanoparticles in Organic Solutions
      Canzi, Gabriele; Mrse, Anthony A.; Kubiak, Clifford P.
      Journal of Physical Chemistry C (2011), 115 (16), 7972-7978CODEN: JPCCCK; ISSN:1932-7447. (American Chemical Society)
      Diffusion-ordered spectroscopy is used to det. gold nanoparticle sizes. Traditional characterization of nanoparticles has centered on imaging by electron microscopy and plasmon resonance absorption in UV-visible electronic spectra. The authors present a convenient method to characterize gold nanoparticles using diffusion-ordered NMR spectroscopy (DOSY). 2-dimensional DOSY NMR is used to calc. diffusion consts. and the diam. of solubilized gold nanoparticles capped with 1-dodecanethiol (C12) or 1-octanethiol (C8) in three deuterated solvents. The distributions of nanoparticle sizes strongly correlate with TEM image anal. C12 and C8 capped nanoparticle sizes are 4.6 and 2.7 nm by TEM as compared to ests. of 4.6 ± 0.3 and 2.5 ± 0.1 nm based on 2-dimensional DOSY NMR data. Reliable size characterization of nanoparticles with NMR active nuclei (1H in this study) in their protective groups (alkane thiols in this study) can be achieved by a widely available NMR method (DOSY) in place of electron microscopy.
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    41. 41
      Pascal, S. M.; Yamazaki, T.; Singer, A. U.; Kay, L. E.; Forman-Kay, J. D. Structural and dynamic characterization of the phosphotyrosine binding region of an Src homology 2 domain-phosphopeptide complex by NMR relaxation, proton exchange, and chemical shift approaches. Biochemistry 1995, 34, 11353– 11362,  DOI: 10.1021/bi00036a008
      41
      Structural and Dynamic Characterization of the Phosphotyrosine Binding Region of an Src Homology 2 Domain-Phosphopeptide Complex by NMR Relaxation, Proton Exchange, and Chemical Shift Approaches
      Pascal, Steven M.; Yamazaki, Toshio; Singer, Alex U.; Kay, Lewis E.; Forman-Kay, Julie D.
      Biochemistry (1995), 34 (36), 11353-62CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)
      Arginine side chains are often involved in protein-protein and protein-nucleic acid interactions. Due to a no. of factors, resonance assignment and detection of NOEs involving the arginine side chains via std. NMR techniques can be difficult. The authors present here an approach to characterization of the interaction between a phosphopeptide (pY1021) and four arginine residues that line the phosphotyrosine-binding pocket of the C-terminal SH2 domain of phospholipase C-γ1 (PLCC SH2). Previously published NOE data provide a partial description of this interaction, including contacts between the aliph. region of Arg 59 and the phosphotyrosine (pTyr) arom. ring. Further characterization has now been accomplished by using 15N and 13C NMR relaxation studies of arginine Νε and Cζ spins, resp., and proton exchange rates of arginine Hε nuclei. Differences between the chem. shifts of the arginine guanidino groups of the free SH2 domain in imidazole and phosphate buffers or in complex with pY1021 have provided insight into specific interactions with the phosphate and the arom. ring of the pTyr. The resulting data are consistent with the most stable hydrogen bonds to phosphate donated by the Arg 39 ε-NH and the two Arg 37 η-NH2 groups and with pTyr arom. ring interactions involving the Arg 39 and possibly the Arg 18 guanidino groups.
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    42. 42
      Yamazaki, T.; Pascal, S. M.; Singer, A. U.; Forman-Kay, J. D.; Kay, L. E. NMR pulse schemes for the sequence-specific assignment of arginine guanidino 15N and 1H chemical shifts in proteins. J. Am. Chem. Soc. 1995, 117, 3556– 3564,  DOI: 10.1021/ja00117a025
      42
      NMR Pulse Schemes for the Sequence-Specific Assignment of Arginine Guanidino 15N and 1H Chemical Shifts in Proteins
      Yamazaki, Toshio; Pascal, Steven M.; Singer, Alex U.; Forman-Kay, Julie D.; Kay, Lewis E.
      Journal of the American Chemical Society (1995), 117 (12), 3556-64CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      A family of 2D NMR expts. is presented for the sequence-specific assignment of arginine guanidino 1H and 15N chem. shifts on the basis of transfer of magnetization exclusively by scalar connectivities. Because of the potential for significant exchange with water at the ε and η positions along the side chain of arginine residues, care has been taken to minimize satn. and dephasing of water throughout the course of the pulse schemes. Attempts are made to minimize the effects of chem. exchange due to moderately slow rotation about the Nε-Cζ bond of arginine. The methods are demonstrated on a 1.5 mM sample of the C-terminal SH2 domain from phospholipase-Cγ1 in complex with a 12-residue phosphotyrosyl peptide comprising its high-affinity binding site in the platelet-derived growth factor receptor.
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    43. 43
      Feng, M.-H.; Philippopoulos, M.; MacKerell, A. D.; Lim, C. Structural Characterization of the Phosphotyrosine Binding Region of a High-Affinity SH2 Domain–Phosphopeptide Complex by Molecular Dynamics Simulation and Chemical Shift Calculations. J. Am. Chem. Soc. 1996, 118, 11265– 11277,  DOI: 10.1021/ja961530r
      43
      Structural Characterization of the Phosphotyrosine Binding Region of a High-Affinity SH2 Domain-Phosphopeptide Complex by Molecular Dynamics Simulation and Chemical Shift Calculations
      Feng, Ming-Hsiang; Philippopoulos, Marios; MacKerell, Alexander D., Jr.; Lim, Carmay
      Journal of the American Chemical Society (1996), 118 (45), 11265-11277CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      Three mol. dynamics simulations of the free, phosphate ion-bound and phosphopeptide-bound C-terminal SH2 domain of phospholipase C-γ1 (PLCC·pY) have been performed to aid in the interpretation of chem. shift data and the elucidation of interat. interactions at the phosphotyrosine (pTyr) binding region. The simulation of the phosphopeptide complex was carried out with newly developed CHARMM force-field parameters for pTyr, optimized against exptl. data and ab initio calcns. The lack of NOEs involving phosphate in the binding pocket had necessitated a chem. shift anal. of the pTyr binding region for a more detailed characterization of the hydrogen bonding interactions involving pTyr. Although most of these interactions are not present in the NMR structure used as the simulation starting point, the system converges early in the simulation to a structure more compatible with the chem. shift data. This is supported by ab initio detn. of the 1Hη and 1Hε chem. shifts of the three arginines (Arg 18, 37, and 39) in the pTyr binding pocket based on the PLCC· pY MD structure, which are in accord with the exptl. values. The simulation structure of the PLCC·pY complex reveals a more complete picture of interat. interactions in the pTyr binding pocket than is possible with current chem. shift and NOE approaches alone, thereby permitting the identification of the primary pTyr-recognition residues. This pattern of interactions is strikingly similar to those of crystal structures of related SH2 domains. The simulations also suggest several alternative interpretations of the chem. shift data to those suggested in the exptl. investigation (Pascal, S. M., et al. Biochem. 1995, 34, 11353). This insight is valuable as the obsd. chem. shifts could result from a no. of possible pictures of interactions. The present study demonstrates that the combination of mol. dynamics simulations and ab initio chem. shift calcns. can enhance the hydrogen-bonding, amino-arom., and aliph.-arom. information content of NOE- and chem.-shift-based protein structures and serve as a complementary tool for the interpretation of chem. shift data at the at. level.
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    44. 44
      Gargaro, A. R.; Frenkiel, T. A.; Nieto, P. M.; Birdsall, B.; Polshakov, V. I.; Morgan, W. D.; Feeney, J. NMR Detection of arginine-ligand interactions in complexes of lactobacillus casei dihydrofolate reductase. Eur. J. Biochem. 1996, 238, 435– 439,  DOI: 10.1111/j.1432-1033.1996.0435z.x
      44
      NMR detection of arginine-ligand interactions in complexes of Lactobacillus casei dihydrofolate reductase
      Gargaro, Angelo R.; Frenkiel, Thomas A.; Nieto, Pedro M.; Birdsall, Berry; Polshakov, Vladimir I.; Morgan, William D.; Feeney, James
      European Journal of Biochemistry (1996), 238 (2), 435-439CODEN: EJBCAI; ISSN:0014-2956. (Springer)
      1H-NMR and 15N-NMR signal assignments have been made for the eight arginine residues in Lactobacillus casei dihydrofolate reductase in its binary complex with methotrexate and in its ternary complex with methotrexate and NADPH. 1H-NMR chem. shifts for the guanidino groups of two of the arginines (Arg57 and Arg43) were sensitive to different modes of binding of the guanidino groups with charged oxygen atoms of the ligands. In the complexes formed with methotrexate, Arg57 showed four nonequivalent NHη proton signals indicating hindered rotation about the Nε-Cζ and Cζ-Nη bonds. The NHη12 and NHη22 protons showed large downfield shifts, which would be expected for a sym. end-on interaction of these protons with the charged oxygen atoms of a carboxylate group in methotrexate. These effects were not obsd. for the complex formed with trimethoprim, which does not contain any carboxylate groups. In the complex formed with NADPH present, Arg43 showed a large downfield chem. shift for its NHε proton and a retardation of its rate of exchange with water. This pattern of deshielding contrasts with that detected for Arg57 and is that expected for a side-on interaction of the guanidino group protons with charged oxygen atoms of the ribose 2'-phosphate group of NADPH.
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    45. 45
      Nieto, P. M.; Birdsall, B.; Morgan, W. D.; Frenkiel, T. A.; Gargaro, A. R.; Feeney, J. Correlated bond rotations in interactions of arginine residues with ligand carboxylate groups in protein ligand complexes. FEBS Lett. 1997, 405, 16– 20,  DOI: 10.1016/s0014-5793(97)00147-6
      45
      Correlated bond rotations in interactions of arginine residues with ligand carboxylate groups in protein ligand complexes
      Nieto, Pedro M.; Birdsall, Berry; Morgan, William D.; Frenkiel, Thomas A.; Gargaro, Angelo R.; Feeney, James
      FEBS Letters (1997), 405 (1), 16-20CODEN: FEBLAL; ISSN:0014-5793. (Elsevier)
      The 1H/15N HSQC NMR spectra of complexes of Lactobacillus casei dihydrofolate reductase contg. methotrexate recorded at 1°C show four resolved signals for the four NHη protons of the Arg57 residue. This is consistent with hindered rotation in the guanidino group resulting from interactions with the α-carboxylate of methotrexate. Increasing the temp. causes exchange line-broadening and coalescence of signals. Rotation rates for the NεCζ and CζNη bonds have been calcd. from lineshape anal. and from zz-HSQC exchange expts. The interactions between the methotrexate α-carboxylate group and the Arg57 guanidino group decrease the rotation rates for the NεCζ bond by about a factor of 10 and those for the CζNη bonds by more than a factor of 100 with respect to their values in free arginine. Furthermore, the relative rates of rotation about these two bonds are reversed in the protein complexes compared with their values in free arginine indicating that there are concerted rotations about the NεCζ bond of the Arg57 guanidino group and the C'Cα bond of the glutamate α-carboxylate group of methotrexate.
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    46. 46
      Morgan, W. D.; Birdsall, B.; Nieto, P. M.; Gargaro, A. R.; Feeney, J. 1H/15N HSQC NMR Studies of Ligand Carboxylate Group Interactions with Arginine Residues in Complexes of Brodimoprim Analogues andLactobacilluscaseiDihydrofolate Reductase. Biochemistry 1999, 38, 2127– 2134,  DOI: 10.1021/bi982359u
      46
      1H/15N HSQC NMR Studies of Ligand Carboxylate Group Interactions with Arginine Residues in Complexes of Brodimoprim Analogs and Lactobacillus casei Dihydrofolate Reductase
      Morgan, William D.; Birdsall, Berry; Nieto, Pedro M.; Gargaro, Angelo R.; Feeney, James
      Biochemistry (1999), 38 (7), 2127-2134CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)
      1H and 15N NMR studies have been undertaken on complexes of Lactobacillus casei dihydrofolate reductase (DHFR) formed with analogs of the antibacterial drug brodimoprim (2,4-diamino-5-(3',5'-dimethoxy-4'-bromobenzyl)pyrimidine) in order to monitor interactions between carboxylate groups on the ligands and basic residues in the protein. These analogs had been designed by computer modeling with carboxylated alkyl chains introduced at the 3'-O position in order to improve their binding properties by making addnl. interactions with basic groups in the protein. Specific interactions between ligand carboxylate groups and the conserved Arg57 residue have been detected in studies of 1H/15N HSQC spectra of complexes of DHFR with both the 4-carboxylate and the 4,6-dicarboxylate brodimoprim analogs. The spectra from both complexes showed four resolved signals for the four NHη protons of the guanidino group of Arg57, and this is consistent with hindered rotation in the guanidino group resulting from interactions with the 4-carboxylate group in each analog. In the spectra of each complex, one of the protons from each of the two NH2 groups and both nitrogens are considerably deshielded compared to the shielding values normally obsd. for such nuclei. This pattern of deshielding is that expected for a sym. end-on interaction of the carboxylate oxygens with the NHη12 and NHη22 guanidino protons. The differences in the degree of deshielding between the complexes of the two structurally similar brodimoprim analogs and the methotrexate indicates that the shielding is very sensitive to geometry, most probably to hydrogen bond lengths. The 1H/15N HSQC spectrum of the DHFR complex with the brodimoprim-6-carboxylate analog does not feature any deshielded Arg NHη protons and this argues against a similar interaction with the Arg57 in this case. It has not proved possible to det. whether the 6-carboxylate in this analog is interacting directly with any residue in the protein. 1H/15N HSQC spectra have been fully assigned for the complexes with the three brodimoprim analogs and chem. shift mapping used to explore interactions in the binding site. The 1H signals of the bound ligands for all three brodimoprim analogs have been assigned. Their 1H chem. shifts were found to be fairly similar in the different complexes indicating that the 2,4-diaminopyrimidine and the benzyl ring are binding in essentially the same binding sites and with the same overall conformation in the different complexes. The rotation rate about the NεCζ bond in the brodimoprim-4,6-dicarboxylate complex with DHFR has been detd. from a zz-HSQC exchange expt., and its value is quite similar to that obsd. in the DHFR·methotrexate complex (24±10 s-1 at 8° and 50±10 s-1 at 15°, resp.). The 1H and 15N chem. shift differences of selected amide and guanidino NH groups, measured between the DHFR complexes, provided further evidence about the interactions involving Arg57 with the 4-carboxylate and 4,6-dicarboxylate brodimoprim analogs.
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    47. 47
      Polshakov, V. I.; Morgan, W. D.; Birdsall, B.; Feeney, J. Validation of a new restraint docking method for solution structure determinations of protein–ligand complexes. J. Biomol. NMR 1999, 14, 115– 122,  DOI: 10.1023/a:1008379225053
      47
      Validation of a new restraint docking method for solution structure determinations of protein-ligand complexes
      Polshakov, Vladimir I.; Morgan, William D.; Birdsall, Berry; Feeney, James
      Journal of Biomolecular NMR (1999), 14 (2), 115-122CODEN: JBNME9; ISSN:0925-2738. (Kluwer Academic Publishers)
      A new method is proposed for docking ligands into proteins in cases where an NMR-detd. soln. structure of a related complex is available. The method uses a set of exptl. detd. values for protein-ligand, ligand-ligand, and protein-protein restraints for residues in or near to the binding site, combined with a set of protein-protein restraints involving all the other residues which is taken from the list of restraints previously used to generate the ref. structure of a related complex. This approach differs from ordinary docking methods where the calcn. uses fixed at. coordinates from the ref. structure rather than the restraints used to det. the ref. structure. The binding site residues influenced by replacing the ref. ligand by the new ligand were detd. by monitoring differences in 1H chem. shifts. The method has been validated by showing the excellent agreement between structures of L. casei dihydrofolate reductase. trimetrexate calcd. by conventional methods using a full exptl. detd. set of restraints and those using this new restraint docking method based on an L. casei dihydrofolate reductase.methotrexate ref. structure.
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    48. 48
      Hajduk, P. J.; Olejniczak, E. T.; Fesik, S. W. One-dimensional relaxation- and diffusion-edited NMR methods for screening compounds that bind to macromolecules. J. Am. Chem. Soc. 1997, 119, 12257– 12261,  DOI: 10.1021/ja9715962
      48
      One-Dimensional Relaxation- and Diffusion-Edited NMR Methods for Screening Compounds That Bind to Macromolecules
      Hajduk, Philip J.; Olejniczak, Edward T.; Fesik, Stephen W.
      Journal of the American Chemical Society (1997), 119 (50), 12257-12261CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      Two one-dimensional 1H NMR techniques for efficiently screening libraries of compds. for binding to macromols. are described that exploit the changes in relaxation or diffusion rates of small mols. which occur upon complex formation. The techniques are demonstrated by detecting ligands that bind to the FK506 binding protein and the catalytic domain of stromelysin in the presence of compds. that do not bind to these proteins. These one-dimensional methods directly detect complex formation between a ligand and a macromol. and thus eliminate false positives often obsd. with other techniques. In addn., since these methods rely on the detection of the uncomplexed compd. rather than the bound ligand or macromol., ligands for macromols. of unlimited size can be detected. Furthermore, active compds. can be directly identified from a mixt., significantly reducing the time and material needed for screening large libraries of compds.
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    49. 49
      Lin, M.; Shapiro, M. J. mixture analysis in combinatorial chemistry. Application of diffusion-resolved NMR spectroscopy. J. Org. Chem. 1996, 61, 7617– 7619,  DOI: 10.1021/jo961315t
      49
      Mixture Analysis in Combinatorial Chemistry. Application of Diffusion-Resolved NMR Spectroscopy
      Lin, Mengfen; Shapiro, Michael J.
      Journal of Organic Chemistry (1996), 61 (21), 7617-7619CODEN: JOCEAH; ISSN:0022-3263. (American Chemical Society)
      Mixt. anal. from a simulated combinatorial split and pool synthesis was accomplished using a new pulse sequence combining LED and TOCSY. Diffusion NMR data were used to decode the individual mols. without the need of prior sepn.
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    50. 50
      Lin, M.; Shapiro, M. J.; Wareing, J. R. Screening mixtures by affinity NMR. J. Org. Chem. 1997, 62, 8930– 8931,  DOI: 10.1021/jo971183j
      50
      Screening Mixtures by Affinity NMR
      Lin, Mengfen; Shapiro, Michael J.; Wareing, James R.
      Journal of Organic Chemistry (1997), 62 (25), 8930-8931CODEN: JOCEAH; ISSN:0022-3263. (American Chemical Society)
      A potential advantage of the pulsed field gradient diffusion NMR method over the chem. shift method is that binding is detected by the observation of the ligand NMR spectrum and not by changes in the receptor NMR spectrum. This should allow the expt. to be tuned to the binding affinity of the ligand by changing the relative receptor concn. This premise was tested by making a mixt. of four carboxylic acids and using the hydroquinine 9-phenanthryl ether as the receptor. The binding consts. for the ligands, and the pKa's are given. As the concn. of hydroquinine 9-phenanthryl ether is increased, the other carboxylic acids, sequentially begin to appear in their order of binding affinity. This demonstrates that the system can be tuned to a desired sensitivity level and that mixts. of compds. contg. only a few components can be screened to select components which bind at a desired level of affinity.
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    51. 51
      Lin, M.; Shapiro, M. J.; Wareing, J. R. Diffusion-Edited NMR–Affinity NMR for Direct Observation of Molecular Interactions. J. Am. Chem. Soc. 1997, 119, 5249– 5250,  DOI: 10.1021/ja963654+
      51
      Diffusion-Edited NMR-Affinity NMR for Direct Observation of Molecular Interactions
      Lin, Mengfen; Shapiro, Michael J.; Wareing, James R.
      Journal of the American Chemical Society (1997), 119 (22), 5249-5250CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      A small mixt. of compds. can be selectively edited to find and identify components involved in mol. interactions using Pulse Field Gradient NMR techniques. The structure of the ligand can be deduced directly, without requiring sepn. of the mixt., using the LED and TOCSY (DECODES) pulse sequence.
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    52. 52
      Bleicher, K.; Lin, M.; Shapiro, M. J.; Wareing, J. R. Diffusion Edited NMR: Screening Compound Mixtures by Affinity NMR to Detect Binding Ligands to Vancomycin. J. Org. Chem. 1998, 63, 8486– 8490,  DOI: 10.1021/jo9817366
      52
      Diffusion Edited NMR: Screening Compound Mixtures by Affinity NMR to Detect Binding Ligands to Vancomycin
      Bleicher, Konrad; Lin, Mengfen; Shapiro, Michael J.; Wareing, James R.
      Journal of Organic Chemistry (1998), 63 (23), 8486-8490CODEN: JOCEAH; ISSN:0022-3263. (American Chemical Society)
      Affinity NMR can be used to produce an edited NMR spectrum that identifies ligands that bind to vancomycin from soln. mixts. contg. nonbinding mols. The Diffusion EnCODEd Spectroscopy (DECODES) expt. performed directly on the same sample can be used to det. the structure of the binding ligands without the need for a phys. sepn. step. The all-D amino acid tetrapeptides DDFA and DDFS, known ligands for vancomycin, were identified in the presence of eight nonbinding tetrapeptides. The bound-ligand signals in the two-dimensional DECODES spectrum are readily identified by comparison with the spectral patterns of the vancomycin cross-peaks in the 2D total correlation spectroscopy and correlation spectroscopy spectra. The screening of soln. mixts. of mols. for direct detection of mol. interactions and structural identification of the interacting ligands provides a powerful new tool to complement methods, such as affinity MS, which rely on the phys. sepn. of mixt. components to identify mol. interactions. The soln. mixts. of compds. for screening by affinity NMR could come from any source where the components are in similar relative amts., including synthesis by combinatorial chem. methods.
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    53. 53
      Anderson, R. C.; Lin, M.; Shapiro, M. J. Affinity NMR: Decoding DNA Binding. J. Comb. Chem. 1999, 1, 69– 72,  DOI: 10.1021/cc980004o
      53
      Affinity NMR: Decoding DNA Binding
      Anderson, Robert C.; Lin, Mengfen; Shapiro, Michael J.
      Journal of Combinatorial Chemistry (1999), 1 (1), 69-72CODEN: JCCHFF; ISSN:1520-4766. (American Chemical Society)
      We have shown that affinity NMR can be used to edit a NMR spectrum so that ligands that have affinity to DNA can be obsd. in the presence of other nonbinding mols. Diffusion encoded spectroscopy (DECODES) can be used to identify the binding ligands. We were able to identify Hoechst 33342 as binding to the Drew-Dickerson dodecamer d(CGCGAATTCGCG)2 in the presence of the nonbinding mols. adenine, adenosine, and thiamine. Affinity NMR appears to be readily applicable to DNA systems for the following reasons. (1) The relaxation rate of the DNA oligonucleotides is favorable, thus the signal intensity loss due to relaxation is not severe. (2) A comparison of the patterns of the DNA cross-peaks upon binding in the two-dimensional total correlation spectroscopy and correlation spectroscopy spectrum are easily performed, and the ligand signals in the two-dimensional DECODES spectrum can be readily identified. (3) The arom. part of the DNA spectrum is devoid of 2D cross-peaks in these correlation spectra, greatly facilitating the interpretation of the bound ligand in the DECODES spectrum.
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    54. 54
      Mayer, M.; Meyer, B. Characterization of ligand binding by saturation transfer difference NMR spectroscopy. Angew. Chem., Int. Ed. 1999, 38, 1784– 1788,  DOI: 10.1002/(sici)1521-3773(19990614)38:12<1784::aid-anie1784>3.0.co;2-q
      54
      Characterization of ligand binding by saturation transfer difference NMR spectroscopy
      Mayer, Moriz; Meyer, Bernd
      Angewandte Chemie, International Edition (1999), 38 (12), 1784-1788CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH)
      The difference between a satn. transfer spectrum and a normal NMR spectrum provides a new and fast method (satn. transfer difference (STD) NMR spectroscopy) to screen compd. libraries for binding activity to proteins. STD NMR spectroscopy of mixts. of potential ligands with as little as 1 nmol of protein yields 1D and 2D NMR spectra that exclusively show signals from mols. with binding affinity. In addn., the ligand's binding epitope is easily identified because ligand residues in direct contact to the protein show much stronger STD signals. For example, the binding specificity of Lewisb-hexasaccharide to Aleulria aurantia agglutinin (AAA) can be mapped to the two fucosyl residues. The efficiency of the STD NMR technique is shown by the binding of N-acetylglucosamine (GlcNAc) to wheat germ agglutinin (WGA).
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