Intramolecular Hydrogen Bonding in ortho-Substituted Arylamide

Sep 1, 2009 - in Philadelphia, 600 South 43rd Street, Philadelphia, PennsylVania 19104-4495, and Polymedix Inc.,. 170 North Radnor Chester Road Suite ...
0 downloads 0 Views 843KB Size
Download PDF
J. Phys. Chem. B 2009, 113, 12809–12815

12809

Intramolecular Hydrogen Bonding in ortho-Substituted Arylamide Oligomers: A Computational and Experimental Study of ortho-Fluoro- and ortho-Chloro-N-methylbenzamides Jhenny F. Galan,† Jodian Brown,† Jayme L. Wildin,† Zhiwei Liu,† Dahui Liu,‡ Guillermo Moyna,† and Vojislava Pophristic*,† Center for Drug Design and DeliVery and Department of Chemistry & Biochemistry, UniVersity of the Sciences in Philadelphia, 600 South 43rd Street, Philadelphia, PennsylVania 19104-4495, and Polymedix Inc., 170 North Radnor Chester Road Suite 300, Radnor, PennsylVania 19087-5280 ReceiVed: June 4, 2009

As a part of our systematic study of foldamer structural elements, we analyze and quantify the conformational behavior of two model compounds based on a frequently used class of aromatic oligoamide building blocks. Combining computational and NMR approaches, we investigate ortho-fluoro- and ortho-chloro-N-methylbenzamide. Our results indicate that the -F substituent in an ortho position can be used to fine-tune the rigidity of the oligomer backbone. It provides a measurably attenuated but still considerably strong hydrogen bond (H-bond) to the peptide group proton when compared to the -OCH3 substituent in the same position. On the other hand, the ortho-Cl substituent does not impose significant restrictions on the flexibility of the backbone. Its effect on the final shape of an oligomer is likely governed by its size rather than by noncovalent intramolecular interactions. Furthermore, the effect of solvent on the conformational preferences of these building blocks has been quantified. The number of intramolecularly H-bonded conformations decreases significantly when going from nonprotic to protic environments. This study will facilitate rational design of novel arylamide foldamers. 1. Introduction Foldamers, synthetic oligomers that fold into well-defined secondary structures,1-3 have attracted considerable attention in the past decade.4-8 They are usually designed to mimic biologically relevant molecules or motifs found in biopolymers, or to fulfill functional requirements such as transport,9-11 molecular recognition,12-16 host-guest chemistry,7,8 and bioactivity.17-21 The structural features of foldamers are often chosen so that noncovalent interactions such as π-π stacking and hydrogen bonding (H-bonding) facilitate specific design goals. Two widely used foldamer classes whose design is based on these interactions are the aromatic oligoamides and oligoureas (Figure 1). The growing interest in these classes of foldamers calls for new structures which are more effective and/or cost less to produce, as well as for a better understanding of the principles that control their shapes and ultimately their function. Aromatic oligoamides with local conformational control provide a platform for introducing a range of flexibility levels through intramolecular H-bonding variations. They consist of aromatic rings connected through peptide bonds (Figure 2). Therefore, elements along the backbone that influence the overall foldamer conformation are the Caromatic-Cpeptide (Ca-Cp), Cpeptide-Npeptide (Cp-Np), and Npeptide-Caromatic (Np-Ca) bonds. Among these, only the Cp-Np bond is inherently rigid. Thus, the conformation of the arylamide oligomers is frequently controlled by regulating the torsional motions around the Ca-Cp and Np-Ca bonds. This is achieved by introducing substituents on the aromatic ring that are capable of H-bonding to the peptide * To whom correspondence should be addressed. E-mail: v.pophri@ usp.edu. † University of the Sciences in Philadelphia. ‡ Polymedix Inc.

N-H group (Figure 2). The position of these substituents and their H-bonding ability are critical in defining the final shape of the foldamer. Thus, a variety of substituents has been used in the design of arylamide foldamers, resulting in different characteristics and applications. As part of a systematic structural study of aromatic oligoamide foldamer building blocks, we have investigated the effects of ortho-substituents of varying H-bonding ability on their conformational preferences.22-24 These and other studies25,26 have pointed out the complexities of the Ca-Cp and Np-Ca torsions. For example, in the case of ortho-methoxy-N-methylbenzamide (Figure 2, 1)22 and ortho-methylthio-N-methylbenzamide (Figure 2, 2),24 we have shown that a significant number of OOCH3 · · · H-N and SSCH3 · · · H-N intramolecular H-bonds are lost in polar protic environments. The intramolecularly H-bonded conformations for 1 in aqueous solution are found in ∼50% of the cases, whereas this value is only 4% for 2. The observed dependence of the conformational distribution on the H-bonding ability of the ortho-substituent as well as the ability to quantify the effect prompted us to undertake further studies on this issue. Foldamers using fluorine-induced stabilization through H-bonding have a prominent place among aromatic oligoamides. For example, fluorine-substituted aromatic amides were reported to form five- and six-membered intramolecularly H-bonded rings, resulting in well-defined secondary structures.7,8,15,27,28 Therefore, rationalizing the effects of ortho-fluoro substitution on the conformational preferences of arylamide building blocks can provide important quantitative information in the design of novel foldamers. While generally deemed a poor H-bond acceptor, chlorine has been reported to form O-H · · · Cl H-bonds in organic alkynols.29 In addition, and given the relative position

10.1021/jp905261p CCC: $40.75  2009 American Chemical Society Published on Web 09/01/2009

12810

J. Phys. Chem. B, Vol. 113, No. 38, 2009

Galan et al. to 122 and 2,24 our study indicates that the retention of intramolecularly H-bonded conformations upon solvation in protic solvents follows the strength of the intramolecular H-bond as it increases in the Cl < SCH3 < F < OCH3 order. On the basis of the dihedral angle distributions observed in the gas phase, chloroform, methanol, and water, these four substituents seem to fall into two groups: the ortho-OCH3 and ortho-F substituents display parallel behavior in all environments, and the same is the case with the ortho-SCH3 and ortho-Cl substituents. Adding to our understanding of what and how structural and electronic features of the arylamide model compounds influence intramolecular H-bonding, our results also allow for proper force field treatment of these types of compounds and enhance our ability to fine-tune the arylamide backbone rigidity.

Figure 1. Examples of aromatic oligoamide and oligourea foldamers. (a) Structure of a helical arylamide foldamer, showing N-H · · · F H-bonds between adjacent units. This particular oligomer was designed as a molecular receptor.7,15 (b) Structure of a typical urea macrocycle,8,43 with H-bonds forming a six-membered ring.

Figure 2. Structure and numbering of ortho-methoxy-N-methylbenzamide (1), ortho-methylthio-N-methylbenzamide (2), ortho-fluoro-Nmethylbenzamide (3), and ortho-chloro-N-methylbenzamide (4). Dashed lines denote intramolecular H-bonds. The Ca-Ca-Cp-Np dihedral angle is marked in red.

of the two elements in the periodic table, results for chlorinated and fluorinated analogues allow for insightful comparisons. In this report, we thus examine in detail the effect of ortho-fluoro and ortho-chloro substituents on the Ca-Cp torsion of aromatic oligoamides in solvents of varying H-bonding ability. Following earlier reports,22,23 our studies employ a combination of quantum mechanics (QM) and molecular dynamics (MD) simulations and NMR experiments on the model compounds ortho-fluoro-N-methylbenzamide (Figure 2, 3) and ortho-chloroN-methylbenzamide (Figure 2, 4). Our results support the previously observed trends regarding the loss of intramolecular H-bonding in protic solvents and the corresponding distribution of conformers with respect to the Ca-Cp bond. In comparison

2. Materials and Methods 2.1. Computational Studies. In order to capture the realistic backbone dynamics in solution with MD simulations, we first determined the ab initio Ca-Cp torsional profile with the orthosubstituents present to accurately take into account the intramolecular environment. Thus, our computational methodology consists of two major parts: QM determination of the torsional potentials in vacuum, followed by MD simulations in solution using a force field modified to reflect the findings of the QM calculations. 2.1.1. Quantum Mechanical Studies. The geometries of 3 and 4 were fully optimized at different levels of theory (HF, MP2, and B3LYP) using basis sets ranging up to 6-311G(3df,2p) (Supporting Information). A convergence study of the optimized geometries of the model compounds, together with our previous results on related compounds 1 and 2, indicated that B3LYP/ 6-311G(d,p) has a similar level of accuracy as the more expensive MP2 method with higher basis sets.22,23 We therefore utilized this level of theory for the analyses. The torsional potential energy profiles were obtained by scanning the Ca-Cp torsional surface in 20° increments. At each scan point, all of the geometrical parameters except the Ca-Ca-Cp-Np dihedral angle were optimized. Torsional barriers were also calculated at other levels of theory used to obtain the equilibrium geometries by constraining the torsional angle that defines the maxima and the minima. All quantum chemical calculations were carried out using Gaussian 03.30 2.1.2. Molecular Dynamics Simulations. All-atom MD simulations were employed to analyze the behavior of the orthosubstituted model compounds in vacuum, chloroform, methanol, and water. The general AMBER force field (GAFF31) with modified torsional parameters was used in the simulations. These were obtained by least-squares fitting to the QM torsional profile described above. It is worth noting that the original GAFF torsional parameter for rotation around the Ca-Cp bond significantly overestimates the barrier of arylamide compounds.23 Partial charges were calculated using the RESP32 method on the optimized geometries of the model compounds. All MD simulations were performed using the AMBER package.33,34 In the presence of solvent, the simulation box size was approximately 30 × 30 × 30 Å3, with ∼500 TIP3P water molecules, ∼400 methanol molecules, or ∼300 chloroform molecules. Periodic boundary conditions and the particle-mesh Ewald (PME)36 method for calculating long-range electrostatic interactions were implemented in the calculations. The solvated systems were equilibrated for 500 ps in the NPT ensemble at 300 K and 1 atm pressure, followed by production NVT runs

ortho-Fluoro- and ortho-Chloro-N-methylbenzamides

J. Phys. Chem. B, Vol. 113, No. 38, 2009 12811

of 5 ns at 300 K. The analysis is based on the last 3 ns segment of the total production trajectory, with a collection interval of 1 ps. 2.2. Synthesis. Benzamides 3 and 4 were prepared from the corresponding acid chlorides and methylamine following standard Shotten-Bauman conditions. Briefly, the chlorides (1 g) were added dropwise to a 40 wt % aqueous solution of methylamine (20 mL), and the resulting mixtures allowed to stir at room temperature for 24 h. The solutions were then acidified to pH ∼2 with 12 M HCl and extracted with ethyl acetate (3 × 30 mL). The combined organic extracts were then washed with water (1 × 30 mL) and dried over anhydrous MgSO4. The solvent was then removed under reduced pressure to yield the final products. N-Methyl-2-fluorobenzamide (3): Obtained as a pale yellow solid in 90.9% yield. mp: 40-42 °C. 1H NMR (400 MHz, CDCl3): δ 8.06 (1H, ddd, J ) 7.8, 4 JHF ) 7.8, J ) 2.0), 7.43 (1H, dddd, J ) 8.3, J ) 7.6, 4JHF ) 5.3, J ) 2.0), 7.22 (1H, ddd, J ) 7.8, J ) 7.6, J ) 1.0), 7.12 (1H, ddd, 3JHF ) 12.2, J ) 8.3, J ) 1.0), 6.78 (1H, bs), 3.05 (3H, dd, J ) 4.8, 6JHF ) 1.1). 13C NMR (100 MHz, CDCl3): δ 164.4 (2JCF ) 2.9 Hz), 161.0 (1JCF ) 246.6), 133.5 (3JCF ) 9.5), 132.4 (3JCF 2.2 Hz), 125.2 (4JCF ) 3.6 Hz), 121.4 (2JCF ) 11.7 Hz), 116.3 (2JCF ) 24.9 Hz), 27.2. N-Methyl-2-chlorobenzamide (4): Obtained as a white crystalline solid in 85.5% yield. mp: 113-116 °C. 1H NMR (400 MHz, CDCl3): δ 7.67 (1H, m), 7.41 (1H, m), 7.35 (1H, ddd, J ) 7.7, J ) 7.3, J ) 2.0), 7.32 (1H, ddd, J ) 7.3, J ) 7.3, J ) 1.5), 6.28 (1H, bs), 3.03 (3H, d, J ) 5.1). 13C NMR (100 MHz, CDCl3): δ 167.7, 135.5, 131.6, 131.0, 130.6, 127.5, 27.2. See the Supporting Information for 1 H chemical shifts for compounds 3 and 4 in methanol and H2O/D2O solution. 2.3. NMR Spectroscopy. One-dimensional nuclear Overhauser effect (1D-NOE) experiments were carried out on a Bruker AVANCE 400 NMR spectrometer equipped with 5 mm BBO and QNP z-gradient probes operating at a 1H frequency of 400.13. Spectra were recorded at 25 °C with the DPFGSENOE pulse sequence of Stott et al.,37 using mixing times of 400, 600, and 800 ms. Selective excitation of specific protons was achieved with Gaussian shaped pulses, the widths of which were calculated from the desired excitation region using the ShapeTool program available within the spectrometer software suite. 2.4. Estimation of Effective Distances. Experimental effective interproton distances were estimated from the NOE enhancements with the following relationship:38

rNOE ) rref

( ) ηref η

1/6

(1)

where ηref is the NOE enhancement measured between a pair of reference protons with fixed geometry and separated by a distance rref and η is the NOE enhancement between the proton pair for which the effective distance rNOE is being estimated. In our calculations, ηref was measured between the N-H and N-CH3 protons and rref was the distance from the amide proton to the centroid of the methyl group (2.48 Å). These estimates were compared to theoretical effective interproton distances, rMD, computed from the MD simulation trajectories using39

rMD ) 〈ri-3〉-1/3

(2)

where 〈...〉 denotes averaging over the trajectories and ri represents the interproton distance measured from individual conformations.

Figure 3. Potential energy profile for the torsion around the Ca-Cp bond in 3 (black) and 4 (red) obtained by scanning the Ca-Ca-Cp-Np dihedral angle in 20° increments. X denotes F or Cl.

TABLE 1: Torsional Barrier for the Ca-Ca-Cp-Np Dihedral Angle in 3 and 4 at Different Levels of Theorya compound

a

level of theory

3

4

HF/6-311G(d,p) HF/6-311G(3df,2p) MP2/6-311G(d,p) MP2/6-311G(3df,2p) B3LYP/6-311G(d,p) B3LYP/6-311G(3df,2p)

7.12 6.67 6.21 6.78 7.49 7.00

6.23 5.87 5.47 5.31 5.86 5.23

Energies are in kcal/mol.

3. Results and Discussion As stated earlier, due to the partial double-bond character of the Cp-Np bond, the flexibility of the arylamide backbone is controlled mainly by the internal rotation around the Ca-Cp and Np-Ca bonds. The results presented in the following sections focus on the Ca-Cp torsion and related conformational preferences for compounds 3 and 4. 3.1. Torsional Potentials. The Ca-Cp torsional barrier for the N-methylbenzamide ranges from 3.5 to 3.9 kcal/mol at different levels of theory.23,40 As expected, upon adding H-bonding acceptors in the ortho position, the barrier increases to 8.7 and 6.7 kcal/mol for 122 and 2,24 respectively. The calculated torsional barrier for 3 is 7.5 kcal/mol, whereas, for 4, it is 5.8 kcal/mol, which is consistent with the increase observed for 1 and 2. The somewhat lower barriers in 3 compared to 1 and in 4 compared to 2 are most probably due to the smaller size of ortho-F and ortho-Cl with respect to the ortho-OCH3 and ortho-SCH3, and hence a weaker repulsive interaction with the CdO oxygen in the conformer with a Ca-Ca-Cp-Np dihedral angle of 180° (Figure 3). In addition, both sF and sCl are known as weaker H-bonding acceptors29,41,42 than sOCH3; hence, a weaker H-bonding stabilization in the equilibrium conformation should be expected. As stated above, the torsional barriers were calculated at different levels of theory and basis sets (Table 1). All of the torsional barrier values were within 1 kcal/mol of the one computed at the MP2/6-311G(3df,2p) level of theory. The torsional profile of 3 (Figure 3) indicates that the minimum energy corresponds to the conformer with a ∠Ca-Ca-Cp-Np of 0°, in which the NsH group points toward the orthosubstituent, optimizing H-bonding between the amide proton and the fluorine atom. In this conformer, the NsH · · · F distance is 1.95 Å, and thus well within H-bonding range. It also corresponds to the lowest energy among all of the conforma-

12812

J. Phys. Chem. B, Vol. 113, No. 38, 2009

tions, and is in agreement with the experimentally observed internuclear distance in a related compound.27 The torsional profile also shows the presence of two maxima, one at a ∠Ca-Ca-Cp-Np of 180° with a corresponding NsH · · · F distance of 4.73 Å and the other at ∼100° showing a NsH · · · F distance of 3.60 Å. These results are consistent with the profile previously obtained for compounds 122 and 2.24 The maximum at a ∠Ca-Ca-Cp-Np of 180° corresponds to the conformation in which the CdO oxygen points toward the F atom, causing steric and electrostatic repulsion and thus increasing the total energy. At a ∠Ca-Ca-Cp-Np of 100°, the aromatic ring π electrons and those from the CdO group are in close proximity, leading to this local maximum. Also, the amide group moves out of the plane of the aromatic ring, thereby decreasing the π electron delocalization of the system. Concomitant to the increase in repulsion and decrease in delocalization as the molecule moves away from the minimum, there is a loss of the stabilizing intramolecular NsH · · · F H-bond, which contributes to the overall energy increase. The ortho-Cl substituted compound shows a somewhat different torsional profile, with the global minimum at a ∠Ca-Ca-Cp-Np of ∼ (40° (Figure 3). In this conformation, the Cl · · · OCdO distance is 4.39 Å, while the Cl · · · N distance is 3.13 Å, an optimal combination of values to minimize the repulsive interaction between the O, Cl, and N atoms. At a ∠Ca-Ca-Cp-Np of 0°, the CdO oxygen moves further away from the Cl atom (4.63 Å) but closer to the amide N (3.07 Å), resulting in a conformation with a slightly higher energy relative to the one at (40°. The maximum energy conformer is again the one with a ∠Ca-Ca-Cp-Np of 180°, in which the CdO oxygen is closest to the ortho-Cl substituent (2.87 Å), hence causing a strong repulsion. Saddle points are observed at ∼ (100°, corresponding to the conformation in which the π electrons of the aromatic ring are in close contact with the electrons of the rotating peptide group. Similar to the ortho-F case, as the molecule undergoes internal rotation, it loses the stabilizing NsH · · · Cl H-bonding interaction and the stabilizing effect of delocalization. 3.2. Molecular Dynamics Simulations. MD simulations of the model compounds were carried out in vacuum, chloroform, methanol, and water to assess the influence of solvents with varying H-bonding ability on intramolecular interactions. As the focus of this work is a realistic assessment of the Ca-Ca-Cp-Np dihedral angle distributions, we relied on our ab initio results to determine the force field torsional parameter for the Ca-Cp bond. The ∠Ca-Ca-Cp-Np torsional parameters we implemented in the GAFF force field are 7.5 kcal/mol for 3 and 5.2 kcal/mol for 4. The analysis of the MD trajectories focused on the Ca-Ca-Cp-Np dihedral angle distributions, as well as on the determination of the balance between intra- and intermolecular H-bonds. In the latter case, an N-H · · · X (X ) F, Cl) H-bond was considered present if the N-H · · · X distance was e2.5 Å for F and 2.6 Å for Cl, and the N-H-X angle was g120°. Two types of interactions with solvent molecules were considered. In the case of protic solvents, H-bonds of both the N-H · · · Osolv and X · · · H-Osolv types were counted. In chloroform, we took into account the contacts between the solute N-H and X groups with the solvent Cl and H atoms, respectively, for comparison purposes. In both cases, the same distance and angle cutoffs detailed above were employed. As shown in Table 2, 79.3 and 78.8% of the conformations of 3 are intramolecularly H-bonded in the gas phase and chloroform, respectively, whereas this value decreases to 55.6%

Galan et al. TABLE 2: Percentages of Conformations in Different Solvent Environments with the Ca-Ca-Cp-Np Dihedral Angle within -60 to 60° (a), Intramolecularly H-Bonded (b), or Intermolecularly H-Bonded with the Solvent (c) compound 3

compound 4

environment

a

b

c

a

b

c

gas phase chloroform methanol water

99.8 99.0 89.6 74.3

79.3 78.8 55.6 43.0

7.3 21.0 59.2

67.5 54.3 21.7 13.5

24.4 18.1 2.9 1.8

18.4 54.4 81.6

in methanol and 43.0% in water. Concomitantly, there is a clear increase in the number of conformations that are intermolecularly H-bonded with the solvent. In chloroform, only 7.3% of the conformations interact with the solvent following the criteria detailed above. In methanol and water, 21.0 and 59.2% of the conformations exhibit H-bonding with bulk solvent molecules, respectively. Clearly, protic solvents strongly compete for H-bonds, and cause a significant loss in the number of intramolecularly H-bonded conformations. Figure 4 shows the Ca-Ca-Cp-Np dihedral angle distributions for conformations of 3 collected from the MD simulations in four different environments. In the gas phase, nearly all conformers have a ∠Ca-Ca-Cp-Np within -60 to 60° (99.8%). A similar behavior is observed in chloroform, an aprotic solvent (Table 2). On the other hand, methanol causes the number of conformers in this region of dihedral angle space to drop to 89.6%. In water, the strongest H-bonding solvent considered, this value decreases further to 74.3%, indicating that a quarter of all conformers of 3 adopt a conformation in which the ortho-F substituent and the N-H group point away from each other. We will refer to these as “reverse” conformations for the remainder of the manuscript. Not surprisingly, all of the conformations that are H-bonded have Ca-Ca-Cp-Np dihedral angles within the -60 to 60° window. Similar conclusions on the effect of solvent can be derived for 4 (Figure 5). As the environment changes from vacuum to water, the percentage of intramolecularly H-bonded conformations goes form 24.4 to 1.8 (Table 2). Intermolecular H-bonding is more prominent in this case, with 18.4% of the conformers involved in interactions with the solvent in chloroform, 54.4% in methanol, and 81.6% in water. The dihedral angle distribution again shifts toward the reverse conformation when going from nonpolar to polar protic environments (Table 2). The difference in the overall shape of the Ca-Ca-Cp-Np dihedral angle distribution between 3 and 4 can be explained

Figure 4. Ca-Ca-Cp-Np dihedral angle distribution of compound 3 in vacuum (black), chloroform (red), methanol (blue), and water (green).

ortho-Fluoro- and ortho-Chloro-N-methylbenzamides

Figure 5. Ca-Ca-Cp-Np dihedral angle distribution of compound 4 in vacuum (black), chloroform (red), methanol (blue), and water (green).

Figure 6. 1D-NOE spectra of 3 (left) and 4 (right) obtained upon inversion of the N-H resonance in chloroform (a,b), methanolic (c,d), and aqueous (e,f) solution. A mixing time of 600 ms was employed in all cases.

by the different sizes of the F and Cl atoms. While in the former case the distribution has one peak at 0°, there are two peaks at ∼ -60° and ∼60° for the latter. In compound 4, the strictly planar conformation in which the aromatic ring, the -Cl substituent, and the peptide bond are coplanar is difficult to achieve, and thus, there is only a small probability of finding conformations with a ∠Ca-Ca-Cp-Np of 0°. The departure from planarity, clearly depicted by the maxima in the Ca-Ca-Cp-Np dihedral angle distribution going from ∼ (40° in the gas phase and chloroform to ∼ (60° in methanol and water, indicates that the molecule opens up to facilitate H-bonding with solvent molecules in polar protic environments. 3.3. NMR Studies. As we have recently demonstrated,22 results from computational studies on arylamide building blocks can be readily corroborated using NMR spectroscopy. In particular, NOE enhancements provide ensemble-averaged data regarding interproton distances which can be directly compared to findings derived from MD simulations. Therefore, the conformational preferences of compounds 3 and 4 in all solvents

J. Phys. Chem. B, Vol. 113, No. 38, 2009 12813 considered in the MD studies were investigated using gradientenhanced 1D-NOESY spectroscopy following our reported approach. In chloroform solution, selective irradiation of the amide protons of 3 or 4 leads to no enhancement of any of the aromatic resonances (Figure 6a and b). These observations are consistent with H-bonding between the amide proton and the orthosubstituents, and agree well with the Ca-Ca-Cp-Np dihedral angle distributions derived from MD simulations for both compounds in this solvent. Inversion of the N-H signals in methanolic solutions leads to a barely detectable NOE for the H-6 proton in 3 (η < 0.1%), and to an ∼0.2% enhancement of the corresponding signal in the case of 4 (Figure 6c and d). This is indicative of reverse conformers becoming more populated in this medium, and, as predicted by our computational studies, also suggests that intramolecular H-bonding is stronger in 3 than in 4. Finally, inversion of the N-H protons of either 3 or 4 in water leads to comparable enhancements of the H-6 proton resonances of ∼0.3% (Figure 6e and f), revealing that reverse conformations are significantly populated in this medium, and confirming that aqueous environments lead to a substantial loss of H-bonds between the N-H and the orthosubstituent in both molecules. These results can be further supported by comparison of the effective interproton distances computed from experimental NOE enhancements to those calculated from the MD trajectories through the use of eqs 1 and 2, respectively. As shown in Table 3, there is good semiquantitative agreement between estimations derived from experimental and theoretical data. 4. Conclusions Our combined computational and NMR study sheds light on the conformational preferences of two members of an important class of arylamide foldamer building blocks. Briefly, the data presented here on compounds 3 and 4 show to what extent the nature of the ortho-substituent affects the retention of intramolecularly H-bonded conformations upon dissolution in protic solvents. In combination with the other two model compounds studied previously by our group,22-24 the results indicate that OCH3, SCH3, F, and Cl orthosubstituents fall broadly into two categories (Table 4). In the gas phase, compounds 1 and 3 are primarily in the H-bonded conformation, as expected. On the other hand, compounds 2 and 4 exhibit higher Ca-Cp bond flexibility in Vacuo, as only 28.8 and 24.4% of all conformations are intramolecularly H-bonded, respectively. In methanol, the number of reverse conformations increases in all four molecules. The effect is very pronounced in aqueous solution. Indeed, compound 1, which bears the strongest H-bonding ortho-substituent, loses about a third of its intramolecularly H-bonded conformations with respect to the gas phase. The percentage of intramolecularly H-bonded conformations in aqueous solution is 51.7% for 1, 43.0% for 3, 3.7% for 2,

TABLE 3: Effective N-H T H-6 Inter-Proton Distances Computed from NOE Enhancements and MD Trajectories for Compounds 3 and 4 compound 3 solvent chloroform methanol water a

η

a

0.03-0.04 0.24-0.31

a

compound 4

rNOE (Å)

rMD (Å)

η

rNOE (Å)

rMD (Å)

4.30-4.36 3.02-3.14

4.31 3.76 3.12

0.21-0.22 0.23-0.29

3.18-3.23 3.05-3.15

3.52 2.97 2.80

The range of η values obtained form 1D-NOE experiments recorded with mixing times of 400-800 ms, as well as the corresponding range of rNOE estimations, are presented.

12814

J. Phys. Chem. B, Vol. 113, No. 38, 2009

Galan et al.

TABLE 4: Percentage of Intramolecularly H-Bonded Conformations of 1, 2, 3, and 4 in Vacuum, Methanol, and Water compound

vacuum

methanol

water

1 2 3 4

79.6 28.8 79.3 24.4

66.5 5.2 55.6 2.9

51.7 3.7 43.0 1.8

and only 1.8% for 4. Thus, the large ortho-substituents with poor H-bonding ability have a negligible effect on the increase in rigidity of the Ca-Cp bond with respect to the nonsubstituted compounds, especially in competing Hbonding environments. Conversely, the ortho-OCH3 and ortho-F substituents can be used for fine-tuning of the Ca-Cp rigidity, as they provide two distinct levels of intramolecular H-bond retention in protic solvents. In addition, the results show how the ortho-substituent and the solvent can regulate the most likely Ca-Ca-Cp-Np dihedral angle that these blocks will adopt. While this angle is centered around 0° in 1 and 3, implying that the model compounds are planar, 2 and 4 have their Ca-Cp distributions centered at (40 and (60°, respectively. Furthermore, the conformational distribution is on each side narrower by ∼10° for 1 than for 2, indicating less departure from planarity for the former. As 1, 2, and 3 are used as building blocks in foldamers whose final shape depends strongly on local conformational control,1 we expect this type of information to be useful for design purposes. One of the main outcomes of the work presented here is that it confirms the ability of our previously postulated approach to accurately quantify the conformational behavior of this class of oligoamide building blocks in different environments. This study is part of a systematic investigation we are undertaking on various types of ortho-substituents already used for tuning the rigidity of backbones containing Ca-Cp bonds, as well as others which can potentially be employed for this task. While there are many interactions that ultimately balance out and result in the final oligomer backbone conformation, the ability to quantitatively compare various monomer choices with respect to specific interactions should facilitate the arylamide foldamer design process. Acknowledgment. The authors recognize the support from the State of Pennsylvania KISK program, the NSF CCLIA&I and MRI programs, Polymedix, Inc. (J.F.G., Z.L., and V.P.), and the Camille and Henry Dreyfus Foundation (G.M.). Supporting Information Available: Chemical shift data in chloroform, methanol, and H2O/D2O solution, convergence study of geometrical parameters, and partial changes used in the MD simulations. This material is available free of charge via the Internet at http://pubs.acs.org. References and Notes (1) Hecht, S.; Huc, I. Foldamers: Structure, Properties, and Applications; Wiley-VCH: Weinheim, 2007. (2) Hill, D. J.; Mio, M. J.; Prince, R. B.; Hughes, T. S.; Moore, J. S. Chem. ReV. 2001, 101, 3893–4012. (3) Gellman, S. H. Acc. Chem. Res. 1998, 31, 173–180. (4) Goodman, C. M.; Choi, S.; Shandler, S.; DeGrado, W. F. Nat. Chem. Biol. 2007, 3, 252–262. (5) Gong, B. Acc. Chem. Res. 2008, 41, 1376–1386. (6) Huc, I. Eur. J. Org. Chem. 2004, 1, 7–29. (7) Li, Z.-T.; Hou, J.-L.; Li, C. Acc. Chem. Res. 2008, 41, 1343–1353. (8) Li, Z.-T.; Hou, J.-L.; Li, C.; Yi, H.-P. Chem.sAsian J. 2006, 1, 766–778.

(9) Potocky, T. B.; Menon, A. K.; Gellman, S. H. J. Biol. Chem. 2003, 278, 50188–50194. (10) Deshayes, S.; Morris, M. C.; Divita, G.; Heitz, F. Cell. Mol. Life Sci. 2005, 62, 1839–1849. (11) Bautista, A. D.; Craig, C. J.; Harker, E. A.; Schepartz, A. Curr. Opin. Chem. Biol. 2007, 11, 685–692. (12) Gelman, M. A.; Richter, S.; Cao, H.; Umezawa, N.; Gellman, S. H.; Rana, T. M. Org. Lett. 2003, 5, 3563–3565. (13) Sadowsky, J. D.; Murray, J. K. Y.; Tomita, Y.; Gellman, S. H. ChemBioChem 2007, 8, 903–916. (14) Dervan, P. B.; Edelson, B. S. Curr. Opin. Struct. Biol. 2003, 13, 284–299. (15) Li, C.; Ren, S.-F.; Hou, J.-L.; Yi, H.-P.; Zhu, S.-Z.; Jiang, X.-K.; Li, Z.-T. Angew. Chem., Int. Ed. 2005, 44, 5725–5729. (16) Hou, J.-L.; Shao, X.-B.; Chen, G.-J.; Jiang, X.-K.; Li, Z.-T. J. Am. Chem. Soc. 2004, 126, 12386–12394. (17) Choi, S.; Clements, D. J.; Pophristic, V.; Ivanov, I.; Vemparala, S.; Bennett, J. S.; Klein, M. L.; Winkler, J. D.; DeGrado, W. F. Angew. Chem., Int. Ed. 2005, 44, 6685–6689. (18) Liu, D.; Choi, S.; Chen, B.; Doerksen, R. J.; Clements, D. J.; Winkler, J. D.; Klein, M. L.; DeGrado, W. F. Angew. Chem., Int. Ed. 2004, 43, 1158–1162. (19) Liu, D.; DeGrado, W. F. J. Am. Chem. Soc. 2001, 123, 7553– 7559. (20) Yin, H.; Frederick, K. K.; Liu, D.; Wand, A. J.; DeGrado, W. F. Org. Lett. 2006, 8, 223–225. (21) Violette, A.; Fournel, S.; Lamour, K.; Chaloin, O.; Frisch, B.; Briand, J.-P.; Monteil, H.; Guichard, G. Chem. Biol. 2006, 13, 531–538. (22) Liu, Z.; Remsing, R. C.; Liu, D.; Moyna, G.; Pophristic, V. J. Phys. Chem. B 2009, 113, 7041–7044. (23) Pophristic, V.; Vemparala, S.; Ivanov, I.; Liu, Z.; Klein, M. L.; DeGrado, W. F. J. Phys. Chem. B 2006, 110, 3517–3526. (24) Liu, Z.; Remsing, R. C.; Moyna, G.; Pophristic, V. “A combined computational and NMR study of torsional motions and hydrogen bonding in ortho-substituted arylamides: Applications in molecular mechanics force fields parameterization and implications for the design of arylamide foldamers”; 236th ACS National Meeting, 2008, Philadelphia, PA. (25) Doerksen, R. J.; Chen, B.; Liu, D.; Tew, G. N.; DeGrado, W. F.; Klein, M. L. Chem.sEur. J. 2004, 10, 5008–5016. (26) Doerksen, R. J.; Chen, B.; Klein, M. L. Chem. Phys. Lett. 2003, 380, 150–157. (27) Zhu, Y.-Y.; Wu, J.; Li, C.; Zhu, J.; Hou, J.-L.; Li, C.-Z.; Jiang, X.-K.; Li, Z.-T. Cryst. Growth Des. 2007, 7, 1490–1496. (28) Zhao, X.; Wang, X.-Z.; Jiang, X.-K.; Chen, Y.-Q.; Li, Z.-T.; Chen, G.-J. J. Am. Chem. Soc. 2003, 125, 15128–15139. (29) Banerjee, R.; Desiraju, G. R.; Mondal, R.; Howard, J. A. K. Chem.sEur. J. 2004, 10, 3373–3383. (30) Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03; revision B.05; Gaussian, Inc.: Wallingford, CT, 2004. (31) Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. J. Comput. Chem. 2004, 25, 1157–1174. (32) Cieplak, P.; Cornell, W. D.; Bayly, C.; Kollman, P. A. J. Comput. Chem. 1995, 16, 1357–1377. (33) Case, D. A.; Darden, T. A.; Cheatham, T. E. I.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Crowley, M.; Walker, R. C.; Zhang, W.; Gohlke, K. M.; Yang, L.; Tan, C.; Mongan, J.; Hornak, V.; Cui, G.; Mathews, D. H.; Seetin, M. G.; Sagui, C.; Babin, V.; Kollman, P. A. AMBER 9; University of California: San Francisco, CA, 2006. (34) Pearlman, D. A.; Case, D. A.; Caldwell, J. W.; Ross, W. S.; Cheatham, T. E.; DeBolt, S.; Ferguson, D.; Seibel, G.; Kollman, P. Comput. Phys. Commun. 1995, 91, 1–41. (35) Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179–5197. (36) Darden, T. A.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089–10092.

ortho-Fluoro- and ortho-Chloro-N-methylbenzamides (37) Stott, K.; Keeler, J.; Van, Q. N.; Shaka, A. J. J. Magn. Reson. 1997, 125, 302–324. (38) Neauhaus, D.; Williamson, M. P. The nuclear OVerhauser effect in structural and conformational analysis; VCH Publishers: New York, 1989. (39) Kessler, H.; Griesinger, C.; Lautz, J.; Mueller, A.; Van Gunsteren, W. F.; Berendsen, H. J. C. J. Am. Chem. Soc. 1988, 110, 3393–3396. (40) Vargas, R.; Garza, J.; Dixon, D.; Hay, B. P. J. Phys. Chem. A 2001, 105, 774–778.

J. Phys. Chem. B, Vol. 113, No. 38, 2009 12815 (41) Howard, J. A. K.; Hoy, V. J.; O’Hagan, D.; Smith, G. T. Tetrahedron 1996, 52, 12613–12622. (42) Dunitz, J. D. ChemBioChem 2004, 5, 614–621. (43) Zhang, A.; Han, Y.; Yamato, K.; Zeng, X. C.; Gong, B. Org. Lett. 2006, 8, 803–806.

JP905261P