Predicting Conformations and Orientations Presentation

Predicting conformations and orientations of guests within a water soluble host: a molecular docking approach


Abstract In this study we have examined conformations and orientations of guests within a water-soluble host known by the trivial name Octa Acid (OA). Docking program Vina, which was originally developed for screening drug-like molecules, has been used to identify binding modes and affinities of select guest molecules with OA. Hydrophobic guests were encapsulated into the nonpolar cavity of OA capsule owing to solvophobic interactions. Amphiphilic guests were bound by keeping the nonpolar part within the cavity of OA, while pointing the polar anionic group out of the cavity. All these results obtained from the docking study were in accord with experimental findings. The post-complexation attributes of the guests were regulated by available free space and the specific interactions between guest–OA pair, which led to unusual conformations and orientations. This study showed that scoring function available with Vina, which was derived from protein–ligand data set, could successfully predict postcomplexed structural features of guests within OA, thus opening opportunities to modulate physical and chemical behavior of guest molecules.

Keywords Water soluble host · Host–guest complex · Conformation · Molecular docking · Binding free energy

Electronic supplementary material The online version of this article (doi:10.1007/s10847-017-0707-7) contains supplementary material, which is available to authorized users.

* Rajib Choudhury

1 Department of Physical Sciences, Arkansas Tech University, Russellville, AR 72801, USA


Water soluble hosts provide extensive opportunities for catalysis, drug delivery, removal of pollutants, sensor design, and for manipulating chemical reactions in a controlled manner [1–6]. Typically, these molecules are equipped with well-defined cavities where target molecules (guest) self-assemble via solvophobic interactions [6–8]. The extent of binding primarily depends on complementary size/shape of host–guest pair and between their specific interactions such as, van der Waals interactions, π···π interactions, and hydrogen or halogen bonding interactions [9–12]. In past three decades, better understandings of these interactions as well as advent of new scientific tools have led to generation and commercialization of many hosts. However, scientific exploitation and application of hosts are limited to experimental screening which requires synthesis of guests with little or no prior knowledge of their self-assembly properties. And that makes this process costly and laborious. Therefore, a rapid in silico identification of suitable guest for a host would be very useful to the experimentalists that would allow further application of the existing hosts in many fundamental and applied research areas.

Herein, we are mainly concerned with in silico prediction of conformations and orientations of guests within a water-soluble host, trivially known as Octa Acid (OA, Fig. 1) [13]. OA forms complexes of composition 1:1 (host: guest) with amphiphilic guests (Fig. 1) [14]. But, it distinguishes itself from other contemporary hosts for its capsule formation property; a process where two OA can envelop guest(s) within its hydrophobic pocket (Fig. 1) [14]. Upon encapsulation, flexible guests with rotatable bonds adopt unusual conformations mainly governed by multiple interactions between OA and guests [15]. For rigid guests,

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word image 3375

Fig. 1 a OA capsule and cavitand, b OA capsule and cavitand within the search space (capsule box dimensions: 28 × 22 × 24 Å3, cavitand box dimensions: 20 × 24 × 22 Å3)

post-encapsulated orientations result from specific interactions and complementary fitting with the cavity [15]. These unusual conformations and diverse orientations prompted several research groups to manipulate photochemical reactions of guests within OA [16–19]. A wide-ranging photoreactions such as, cycloaddition, cistrans isomerization, oxidation, cyclization and cleavage have been reported with great control in product selectivity [16, 17]. Moreover, OA can donate energy, electron, and hydrogen to a bound guest, a property which makes OA a unique host [17]. But, outcome of all of the reactions depends on OA influenced conformation and pre-orientation of guests, as well as on available free space within the OA.

In a typical project, guests are prepared and characterized in wet-labs. Complexation of OA and guest is achieved by adding a solution of guest into the aqueous solution of OA. The first sign of host–guest complexation is usually obtained from 1H NMR experiment. Qualitative information about orientation/conformation of guest is also obtained from the same experiment. More detailed three dimensional structural features of complexed guest are extracted from two-dimensional 1H NMR analysis and molecular modelling. And an overall conclusion about a specific chemical event is drawn from 1H NMR (1D and 2D), molecular modelling, and other supporting experiments.

Thus, the above time-consuming and unpredictable host–guest complex preparation process prompted us to investigate guest complexation with host OA by molecular docking in hope of transferring the knowledge of virtual screening to the synthetic supramolecular host–guest systems. Our goal was to obtain optimized parameters for OA and guests and utilize a docking program to predict orientations, conformations, and binding affinities of guests. We believe the information obtained from these results will assist us and other experimentalists to design new guest molecules and predict outcome of a reaction in a cost-effective way.

Herein, we report the docking results of 52 select host–guest complexes obtained by using docking program Vina [20]. Guest molecules with available experimental complexation data were chosen for this study to get an insight into the applicability of the optimized scoring function available with Vina. All the docking results were compared, in a complementary fashion, with published 1H NMR (1D and 2D) determined host–guest structures, molecular modelling data, as well as with host-controlled photoproducts of guests. These results show that docking of guests within OA cavitand and capsule can reproduce postencapsulated structural features, i.e., orientations and conformations of guests, as reported in literatures.

Experimental section

Molecular dynamics simulation and preparation of host

Molecular dynamics (MD) simulation was performed using the following multistep strategy. In the first step, OA was optimized with Merck Molecular Force Field (MMFF) available on Spartan 03 program [21]. It was then simulated for 40 ns in explicit water utilizing OPLS-AA force field on GROMACS 5.1.1 program [22–24]. The time period for simulation was set based on root mean square deviation (RMSD) analysis. Guests were optimized using Chem3D program with MM2 force field. Topologies of the host and guests were prepared by using MKTOP program [25]. Partial charges of host and guest were generated from ESP charge fitting using the ChelpG method at the B3LYP/6-31G* level on Gaussian program [26–29]. In the next step, guest and hosts were placed in a cubic (40 × 40 × 40 Å3) simulation box filled with SPC water and 16 sodium ( Na+) ions. After filling the simulation box with water, the potential energy of the starting host–guest assembly was minimized with steepest descent method for 1000 steps. Initial velocities for atoms were assigned according to a Maxwell distribution at 300 K. A periodic boundary condition (PBC) was applied and the equation of motion was integrated at time step of 2 fs using the LEAP-FROG algorithm under the NPT ensemble at 300 K temperature and 1 bar pressure. A non-bond pair list cutoff of 12 Å was used. The bond lengths were constrained using the LINCS algorithm. The long–range electrostatic interactions were calculated by the particle-mesh Ewald method with Verlet cut-off scheme [30]. VMD and Pymol were used for trajectory analysis, visualization and preparation of structural diagrams [31, 32].

Molecular docking

word image 3376Scheme 1 Structures of the guests used in this study

Host–guest molecular dockings were performed on a single CPU Windows-OS computer (64-bit) with 3.30 GHz processor and 8.00 GB of RAM on Vina 1.1.2 program (http://www. The coordinate structures of the guests (Scheme 1) were constructed and optimized with MM2 force field on Chem3D. AutoDock Tools 1.5.6 was used for preparing host and guest input files in pdbqt format, which is a modified protein data bank format containing atomic charges, atom type definitions and, for ligands, topological informations. During input file preparation, Gasteiger partial charges were added to each guest molecule, non-polar hydrogen atoms were merged, and torsional rotatable bonds were defined. All the single bonds were made rotatable, whereas double and triple bonds were kept as rigid (non-rotatable). All other parameters were kept at their default values. However, a rectangular box of dimensions 28 × 22 × 24 and 20 × 24 × 22 Å3 with 1.0 A grid spacing was constructed to encompass the entire host capsule and cavitand, respectively (Fig. 1). The exhaustiveness of each docking was kept at 8 while the seed was varied randomly as generated by the program.

Source of error

A potential source of error was finding the guests outside of the OA capsule and cavitand as the guests were allowed to translate into any region within the search box. But, neither such pose nor any visually deformed molecular conformation was recorded.

Results and discussion

Experimental evidences of host–guest complexes examined in this study have been reported in literatures as detailed in the reference section. Preparation and optimization of host OA have been included in the experimental section. Briefly, three dimensional equilibrated structure of OA was obtained from MD simulation in explicit aqueous solvent utilizing OPLS-AA force field and GROMACS program [22–24]. A capsular assembly with an encapsulated hydrophobic guest was energy-minimized with steepest descent method followed by simulation for 40 ns in water. The equilibrated host-assembly obtained from MD simulation was then treated as receptor (host) for docking. During docking run the host OA was kept rigid while guest molecules (Scheme 1) were treated as flexible ligands. The output of docking results was ranked from highest binding affinity (best pose) to lowest binding affinity energy. In this study, results from best-posed host–guest pairs were compared with experiments, unless stated otherwise.

Orientation and conformation of guests within OA capsule

In this section, we will discuss about conformations and orientations of guests within the host OA (both capsule and cavitand). First set of guests selected for docking were alkenes (1–6), alkynes (7–10) and alkanes (1116). In 2013, with the help of NMR and molecular dynamics simulation Choudhury et al. have demonstrated that depending on chain length and phenyl head group these guests adopt unusual conformations within OA capsule [15]. Guests with shorter alkyl chains encapsulate with extended conformations, whereas guests with longer alkyl chains fold, bend and coil within the narrow space of OA capsule, presumably stabilized by multiple weak non-covalent interactions.

word image 3377Fig. 2 The best-ranked conformers of guests obtained from molecular docking. a 1@OA2, b 7@OA2, c 11@OA2, d 5@OA2, e 9@OA2, f 16@OA2

Similar trends were observed in our present docking study. Short-chain alkenes (1–4) and alkynes (7 and 8) remained in elongated conformation, positioning their phenyl groups and the alkyl chains in two opposite halves of the OA capsule, with methyl groups positioned at the tapered lower part of the OA (Fig. 2, ESM1). But, a different scenario emerged for guests with longer alkyl chains (5, 6, 9, and 10). These guests were included in folded and bent conformations owing to their chain lengths, which were longer than the cavity length of OA capsule (Fig. 2, ESM1). Though bent and folded conformations are not energetically favorable forms for aliphatic chains in organic solvents, these unanticipated conformations within OA are most probably stabilized by non-covalent interactions between the guests with walls of the host.

In case of alkane guests with flexible alkyl chains (1116), orientations and conformations (Fig. 2, ESM2) were also in complete agreement with experimental NMR data. These guests were included positioning their methyl groups at the tapered bottom end of the OA, while the phenyl head groups were held in the wider middle region of the capsule. The alkyl chains were bent and twisted in several places. Unlike the alkenes and alkynes, the plasticity of the alkanes enables the chains to bend and fold at any location, resulting very unusual conformations within the OA capsule. The energy penalties, most probably, get compensated by weak interactions between guests and the walls of hosts.

Second set of compounds were photochemically active guests, which upon irradiation with suitable wavelength of light undergo varieties of reactions [33]. Several research groups in past have demonstrated the effect of free space and confinement produced by OA on the photophysical properties as well as on product distribution of photochemical reactions. One such well-studied reaction is Norrish type I/II of dibenzyl ketones (DBK, 17–28) within organized media such as micelles, cyclodextrins, zeolites, and OA [33].

In this study, all the para-alkyl DBK guests (17–20) were docked within OA capsule and ranked according to their decreasing binding affinities [34, 35]. Figure 3, ESM3 show that in all these conformations, the methyl groups of p-alkyl chains stayed at the tapered end of the OA cavitand, whereas two bulky phenyl groups oriented in the wider middle region of the OA capsule. As the length of the chains increased, they folded and bent pushing both phenyl groups into the deeper part of the other halves of the capsule. In case of α-alkyl DBK guests (21–26), 75% of docked results showed similarity with NMR deduced conformations. For a small to mid-sized guests (methyl to pentyl chains, 2125) the alkyl chains oriented and folded keeping the methyl groups towards the tapered end of the OA cavitand and bulky phenyl groups in the wider middle region of the capsule. But, for guests with elongated chains (hexyl and octyl, 26 and 28), the phenyl groups oriented opposite to each other in two OA hemispheres, while alkyl chains coiled and stayed in one hemisphere. For guest 27, though orientation of phenyl groups was supported by NMR, the conformation of alkyl chain was not [34, 35].

word image 3378Fig. 3 The best-ranked conformers of guests obtained from molecular docking. a 17@OA2, b 20@OA2, c 24@OA2, d 27@ OA2, e 28@OA2, f 34@OA2

Another class of photochemically active guests investigated in this study was 1,4-diaryl-1,3-butadienes (2934). These conjugated dienes can exist in two conformations defined as s-trans and s-cis with respect to the single bond, often called transoid and cisoid. The transoid form being thermodynamically more stable in solution is the predominant isomer (~99%) at equilibrium. Interestingly, after docking of these conjugated dienes within OA capsule, they no longer remain in transoid form; instead most favorable conformers within OA were cisoid (Fig. 3, ESM4). These findings were in complete agreement with the report of Samanta et al. where the authors demonstrated the preferential inclusion of cisoid isomers within the OA capsule [36].

The final set of photochemically active guests studied were carbene and nitrene precursors (3539), which upon illumination with ultraviolet light undergo fast photochemical reactions [37, 38]. NMR experiments, molecular modelling and photochemical product distribution in past have unequivocally shown the thermodynamically stable orientations of these guests within OA cavitand in water. Figure 4 and Figure ESM4 show the best-ranked orientation of each guest within OA, which are similar to literature reported results. Except for guest 35, where the –OH functional group remains at the tapered end of the OA cavitand, which is energetically unfavorable according to the past literature report. We believe water has a major role on equilibrium structure (final orientation) of 35. The enthalpically driven hydrogen bonding interactions would reorient the guest in a way where the –OH functional group can interact with waters at the wider opening of OA cavitand, resulting high enthalpy–entropy compensation.

But, in case of guests 36 and 37, the halide groups located at the tapered end of the OA, probably favored by size-shape complementarity as well as van der Waals type interactions. Similarly, azide-adamantanes (38 and 39) complexed with OA by pointing the azide functional groups at the bottom end of the OA. 1D and 2D NMR data in literature had suggested such orientations too. Moreover, photo-functionalization of these guests with the inner bottom part of the OA was rationalized to such pre-organizations. Thus, Vina successfully predicted not only the conformations of guests within confined space of OA capsule, also the orientations of guests within OA cavitand [39, 40].

Binding free energy prediction

After an overall success on predicting 3D structural features (conformations/orientations) of guests within host OA, we investigated the quantitative aspects of molecular docking, namely binding free energy predicting ability of Vina for OA@guest complexes [39, 40]. For this study, we have selected 13 guest molecules (40–52) whose experimental binding free energies are available in literature [41, 42]. It is well documented that OA form 1:1 complex with amphiphilic guests, and binding constant as high as 1.1 × 106 M−1 at 298 K has been reported for OA and adamantane derivative [38, 41] .

In our study, the predominant binding modes for all these guests were obtained as expected (Fig. 4, ESM5). The anionic carboxylate groups orientated towards the wider opening of OA and the hydrophobic part remained in the deeper cavity (Fig. 4). This particular orientation would be thermodynamically stable as the anionic carboxylate interacts with polar water and at the same time the hydrophobic part of the guest interacts with non-polar inner core of the host by favorable van der Waals type interactions.

word image 3379Fig. 4 The best-ranked conformers of guests obtained from molecular docking. a 35@OA, b 36@OA, c 38@OA, d 40@ OA, e 45@OA, f 52@OA

Moreover, in line with predominant structure predictions, a good correlation (r2 = 0.53) between experimental and predicted binding free energies was observed (Fig. 5). In general, the aliphatic guests bound more strongly than their aromatic homologues presumably due to their more voluminous shapes which reduce the distance between the walls of the host and the guests resulting a snug-fit complex. Interestingly, a high degree of

word image 3380

Fig. 5 Comparison of Vina predicted and experimentally obtained binding free energies (r2 = 0.53) for OA complexes (1:1) with guests (36–48)

Table 1 Experimental and theoretical binding free energies (kcal/ mol) for OA complexes with amphiphilic guests


Experimental binding affinity (kcal/mol)

Theoretical binding affinity (kcal/ mol)








































similarity between experimental and calculated data was observed for conformationally flexible guests. For example, excellent correlation for 50 (−4.9 vs. −5.4), 51 (−6.0 vs. −6.2) and 52 (−6.8 vs. −6.4) was observed since they possessed all rotatable C–C bonds. For cyclic aromatic and aliphatic guests the predicted values were either over- or under-estimated from the experimental values, but deviations were very small (Table 1). Maximum deviation was observed for weak binding guest benzoic acid (41; overestimated by 2.2 kcal). Docking gives an erroneous result probably due to small hydrophobic surface area of 41, lacking a size-shape matching. On the other hand, for puckered and hydrophobic cyclohexanoic acid (46), docking predicts binding affinity with minimal error.


In this study, we have shown that docking program Vina can successfully predict conformations/orientations of guests within a water-soluble host. A total of 52 host–guest pair were docked and the best pose from each pair was compared with NMR, molecular modelling and photochemical reaction data in complementary fashion. Our results have shown that the conformations and orientations of guests within host depend on available free space within host, types of functional group attached with guest, as well as on interactions between host, guest, and solvent. A nonpolar molecule with flexible chains can adopt unusual bent or folded conformations within the microenvironment of host, most likely, stabilized by non-covalent interactions between the host and the guests. Amphiphilic guests form complexes by holding the hydrophobic part within the cone-shaped nonpolar cavity and the anionic carboxylate group at the wider opening of OA, predominantly controlled by polar interactions and overall size-shape complementarity of host–guest pairs.

The quantitative results of docking were also very assuring and a good correlation was observed between experiments and dockings. Though the dockings were performed with random seed generated by machine, the best pose obtained from each study remained same if same configuration parameters were provided [20, 40]. The postcomplexed features of host–guest chemistry will open up many new research areas in fundamental and applied science as self-assembled OA and guests provide opportunities for making new functional materials and have potential to function as anchoring agents for targeted delivery [43, 44]. Thus, a rapid prediction of post-encapsulated conformational or orientational trend will be very handy before embarking on a supramolecular material design journey.

Compliance with ethical standards

Conflict of interest The authors declare that they have no conflict of interest.


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Chem 361 P6-Asynchronous Oral presentation _fall 2020

Project 6: Asynchronous Individual Oral Presentation (45 pts)

You made it through to the final Project of the semester. Congratulations, I know it has been A LOT of work, especially with all of us being at home for so long now and doing everything online. However, I believe you are starting to realize the benefits as your writing, reading, and organizing skills are improved compared to the beginning of the semester. For many students, this Project is stressful and enjoyable. Please know past students have said, after completing their presentations, that it wasn’t as bad as they expected.


The final part of the group projects is the oral presentation of a paper that focuses on your subtopic. To complete your last project for the semester, you will complete the following:

  • As an individual, you will give a presentation of one of your research articles: upload your selected article for approval by your instructor.
    • Essentially, you will present one paper used to write your literature review. This will be one of the 4 additional papers you found that is focused on your subtopic. § Your presentation will be 8 – 10 minutes.
  • Time-management applies to talks whether these are at a conference or seminar, respecting speaking times is essential. Approximate times for each section are suggested below.
    • 1 – 2 minutes: Introduce yourself, the article, the problem, and broader context o 1 – 2 minutes: method/approach used
    • 4 – 5 minutes: results & discussion of data and interpretation o 1 minute: conclusion o In a conversational tone, you will cover approx. 1 slide per minute …
  • PowerPoint slides are required for each oral presentation o Upload the PPT presentation to Dropbox on the day presentations are due (12/7/20).
      • PPT filename format: P6_YourName_PPT_F20.pptx o Upload your video in .mp4 format (only) to a separate Dropbox (due 12/7/20)
      • mp4 filename format: P6_YourName_PPT_F20.mp4
  • Business casual attire is required for the presenters
  • No Zoom backgrounds: find a suitable place in which to give a professional presentation
  • What software should you use to record your presentation?
    • You are free to use Zoom, Camtasia, or other software you are comfortable using o If you are new to this: Zoom is strongly recommended for simplicity
    • Both your slides and the video of you must be showing throughout your presentation

§ In Zoom, the side-by-side format is preferred (50% slides, 50% you!) o Test things out and plan your recoding method well in advance!

    • Make sure your video and text in your PPT are visible on a 12 – 13 inch screen!
  • A grading rubric will be posted, and students will peer-grade each other’s presentations during the class final exam period. You will be assigned 6 to grade during our scheduled final exam time on Dec. 17, 2020 from 8 am to 10 am.
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