Assembling Structures of Barbituric Acid Derivatives on Graphite

Aug 21, 2012 - ... Rui-Hong Duan , Zhi-Yong Yang , Hao-Li Zhang , and Yuan-Ping Yi ... Brandon E. Hirsch , Kevin P. McDonald , Amar H. Flood , Steven ...
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Assembling Structures of Barbituric Acid Derivatives on Graphite Surface Investigated with Scanning Tunneling Microscopy Ting Chen,† Hui-Juan Yan,† Zhi-Yong Yang,‡,* Dong Wang,† and Ming-Hua Liu† †

Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100090, P. R. China ‡ School of Chemistry and Chemical Engineering, Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, P. R. China ABSTRACT: The self-assemblies of three barbituric acid compounds on highly oriented pyrolytical graphite surface were investigated using scanning tunneling microscopy. On graphite surface, 5-(4-N-hexadecylaminobenzylidene))-2,4,6-(1H,3H)-pyrimidinetrione (BA I) pairs together with head−head styles and forms chiral structure with grouping of three molecular pairs as a unit motif. 5-(4-(N,N-Dihexadecylaminobenzylidene))-2,4,6-(1H,3H)-pyrimidinetrione (BA II) also appears as head−head molecular pairs but with slight displacement between each other. The small shift destroys the symmetry of molecular pairs and introduces chirality to the molecular pairs and in turn the formation of chiral domains. In this dense packing arrangement, only one hexadecyl chain of BA II lies on graphite surface, whereas the other one hangs in air. 5-(4-(N-Methyl-N-hexadecylamin obenzylidene))-(1,3-diethyl)-2-thioxodihydro-4,6-pyrimidinedione (BA III) organized into similar structure to BA II. Single molecular lines of BA III could be found in experiments from time to time, which suggests the weak intermolecular interaction due to structure changing in head part of BA III. These results may help us to understand varied self-assembling structure and process involved BA derivatives and other lipid molecules.

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INTRODUCTION Barbituric acid (BA, Scheme 1a) and its derivatives are significantly interesting to bioresearching areas such as new drugs development, artificial biomembranes, biomolecular recognition and assembly, and so on. As for drugs, they are used to cure convulsion, cancer, and inflammation as well as being effective hypnotics with few side effects.1,2 Besides clinic treatment, BA compounds are widely employed in constructing an artificial biomembrane to investigate complicated membrane processes in a living body in a more controllable way.3 Cell membranes play a key role in cell signaling, cell−cell interaction, ion conductivity, and substance transportation in which molecular recognition is usually involved. Furthermore, membranes also serve as an attachment surface for extracellular structure, other cells, and drugs. The biovalue of BA analogues originates from its amphiphile structure and excellent recognition ability. Most BA analogues contain pure alkyl or aromatic alkyl tail working as a lipophile part.4 With the ability of forming multi-hydrogen bond, BA parts work as an hydrophilic head and functional group realizing molecular recognition.5−7 Numbers, length, position, and types of tail parts can be adjusted accurately through an available synthetic process; therefore, properties of whole molecules could be tuned correspondingly.6 Nowadays, numerous BA compounds are designed and synthesized for developing more effective drugs and fabricating artificial biomembranes with the expectation of modeling a living bio process, especially for processes like drug targeting, supra© 2012 American Chemical Society

molecular chirality, molecular recognition, structure deformation of membrane, lipid molecules migration, and so on.1,3,8−10 Most artificial biomembranes in published results were constructed by Langmuir−Blodgett (L-B) technology.7,10−14 Achiral BA derivatives (Scheme 1c, BA II) assembled into chiral L-B film in which molecular structure tilt with the same angle to match the confirmation of hydrogen bonding between neighbor molecules.15 However, chiral structure would be weakened in intensity, even destroyed completely, depending on the amount of other amphiphile molecules added to the system.4 Of all mixing candidates, melamine and its derivatives were the most promising candidate due to its perfect complementary recognition groups with BA.16−20 Investigation shows that BA II/melamine develops into a complex monolayer and appears as regular fibers in LB morphology instead of the spiral structure of BA II alone.5 The hydrogen bond mode was changed by the existence of melamine and is responsible for the outcome. Abundant experiments and simulation verified that modifying the structure of either melamine or BA compounds and the relative ratio of two type of molecules could lead to different hydrogen bonding arrangements and in turn would cause formation of diverse assembly.17,21,22 Incorporated into the biovesicle, BA or melamine derivatives could act as functional molecules to learn the migration of lipid molecules and how the Received: June 5, 2012 Revised: August 15, 2012 Published: August 21, 2012 19349

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Scheme 1. Molecular Structure of BA, BA I, BA II, and BA III

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RESULTS AND DISCUSSION Adsorption of BA I. Figure 1 gives a typical large-scale STM image acquired on the BA I adsorption structure on the

complementary group affects the interaction between vesicle containing either BA derivatives or melamine, respectively.23 Former research suggests that large unilamellar vesicles would aggregate rapidly if integrating with BA derivatives and melamine derivatives correspondingly in respective vesicles, whereas giant unilamellar vesicles have no such effect.3 Only a small amount of published research has been performed on the surface. Study on the graphite surface suggests that the BA derivatives can arrange into a tapelike supramolecular structure maintained by multi-hydrogen bonding between adjacent BA parts.24 Understanding properties of BA derivatives on the surface is as important and interesting as that in solution or L-B film because many processes such as BA drug transportation and targeting, membrane formation, structure changes, and so on may involve BA adsorbing or desorbing on certain kinds of surface. Here we studied the adsorption of several BA derivatives (Scheme 1b−d) on a highly oriented pyrolytic graphite (HOPG) surface using scanning tunneling microscopy (STM). All three molecules pair together in a head−head manner and form a chiral structure, but structure motif of the BA I adlayer is different from that of BA II or BA III adlayer. A single molecular line could be found in the assembly of BA III due to its weak molecule−molecule interaction. Results will help to summarize the relationship between molecular structures and assembling behavior, design and construct artificial biomembrane, and understand BA drug mechanism and membrane process in real life environments.

Figure 1. Typical large-scale STM image of BA I adsorption structure. Tunneling condition: Vbias = 580 mV, Itip = 730 pA.

HOPG surface. Two kinds of rotating angle between neighbor domains can be found in Figure 1: 60° or 120° (pointed out by the black angle in Figure 1); 90° or 150°, as marked by the white arrow angle. The formation of these two kinds of domain angles implies the existence of chiral structure. The symmetry of both types of domain angle follows the typical three-fold structure of HOPG surface, which indicates a strong interaction of BAI-graphite. Domains are featured with an alternating appearance of high- and low-contrast rows. It is reasonable to assign the head part of BA I to bright stripes and the alkyl chain of BA I to low-contrast rows because it is a well-known fact that electronic density on the heads part of BA I is richer than that on alkyl chain. Submolecular STM images (Figure 2) show that long bright stripes are constructed with short bright rods. The length of bright short rods is averaged as 1.5 ± 0.2 nm corresponding to two folds of BA I head parts within experimental errors, which clearly show us that two BA I molecules pair together in a head−head style imaging as a short bright rod. Another notable character in Figure 2a is those short low contrast trenches intercalated among alkyl chain parts periodically. Two black arrows were overlaid on trenches to show them more clearly. Lower contrast even than alkyl chain parts of BA I indicates free occupying of those areas, and obvious periodicity of lowcontrast trenches suggests that the subunit of BA I adlayer is a group of a certain number of BA I pairs instead of a single one. Structural chirality could be further verified by the angle defined as the tilting angle between backbones of BA I molecules and the direction of stripes. Averaged data determines that the BA I backbone rotates 62 ± 2° with strips

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EXPERIMENTAL METHODS 5-(4-N-Hexadecylaminobenzylidene))-2,4,6-(1H,3H)-pyrimidinetrione (BA I, Scheme 1b), 5-(4-(N,N-dihexadecylaminobenzylidene))-2,4,6-(1H,3H)-pyrimidinetrione (BA II, Scheme 1c), and 5-(4-(N-methyl-N-hexadecylaminobenzyl idene))-(1,3-diethyl)-2-thioxodihydro-4,6-pyrimidinedione(BA III, Scheme 1d) were synthesized according to the procedure in literature.25,26 Tetrahydrofuran (THF) was from Aldrich and used as solvent without further purification. The sample was prepared by depositing a drop of solution containing respective molecules with concentration less than 10−4 M on a freshly cleaved HOPG surface. All STM experiments were performed by a Nanoscope IIIa STM (Digital Instruments, Santa Barbara, CA) with mechanically cut Pt/Ir (90/10%) tips. All STM images given in this article were collected with the constant current mode and used with flatten processing. The tunneling conditions for each STM image are given in the corresponding Figure caption. 19350

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Figure 2. (a) High-resolution STM image of BA I adsorption structure. (b) Illustration of adsorbing model of BA I molecules. c) Small-scale STM image of BA adsorption structure. Tunneling conditions: (a) Vbias = 559 mV, Itip = 764 pA, inserted image Vbias = 760 mV, Itip = 684 pA and (c) Vbias = −570 mV, Itip = 694 pA.

molecules. As a well-known fact, the alkyl chain matches the graphite lattice quite well. Therefore, the number of alkyl chains is an important element affecting the adsorption structure. Here we investigated the assembly of BA II and compared it with that of BA I to understand the adsorption behavior of BA derivatives systematically. The large-scale image (Figure 3) reveals that BA II forms relatively smaller domains than that formed by BA I. White

direction clockwise or counter-clockwise, as demonstrated by the angle in Figure 2a and inserted image, respectively. Several BA I molecules were imposed on the left side of Figure 2a with short black rods on the head parts to demonstrate the adsorption confirmation of BA I. In this structure, BA I lies on the surface in a head-to-head manner, whereas intercalated alkyl tails occupy the area between bright stripes. Further work needs to be done to explain the formation of BA I molecular groups. On the basis of the molecular arrangement, the unit cell was deduced and outlined in Figure 2a with parameters a1 = 2.4 ± 0.2 nm, a2 = 4.9 ± 0.2 nm and α = 65 ± 2°. A structure model was tentatively proposed in Figure 2b, showing the hierarchy of structure: BA I first pairs together with head−head style, and then three pairs group into the structure motif of the adsorption adlayer. Two polygons were schemed in Figure 2a,b to indicate the structure motif. The unoccupied region left between motifs corresponds to a low-contrast area in the alkyl chain adsorbing area, as indicated by black arrows in Figure 2a,b. In the left side of Figure 2b, a mirror-reflection of the structure motif model is provided to illustrate the chirality of the BA I structure. After investigation of perfect domains, we moved to the area containing dislocations and acquired high-resolution image carefully. Figure 2c demonstrates a typical dislocation structure as marked out by black arrows. STM images suggest the structure motif shift along the backbone of the BA I molecular pair about half the stripe width. Two black rectangles were superimposed on bright stripes, forming dislocation, which illustrates displacement clearly. The shifting distance is determined to be 0.7 ± 0.2 nm, reasonably consistent with the length of the head part of BA I. The results verify head− head style of BA I molecules inferred from former analysis. Adsorption of BA II. The BA II tail part has two hexadecyl chains, whereas its head part is exactly the same as BA I

Figure 3. Large-scale STM image of BA II. Tunneling conditions: Vbias = 682 mV, Itip = 739 pA.

polygonal lines in Figure 3 mark out a U-shape pattern constructed by several rotated bright stripes in different domains. Similar to BA I adlayer, 60°/120° (white bar angle in Figure 3) and 90°/150° (arrow angle in Figure 3) angles can also be found. Figure 4a represents a high-resolution image of BA II assembly showing single alkyl chain and rod substructure of bright strips. The area contains 60° and 90°-type of rotation angle simultaneously, as denoted with θ and γ in Figure 4a. A small black gap was resolved in the exact center of rod and 19351

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Figure 4. (a) Small-scale STM image of BA II adlayer. Tunneling conditions: Vbias = 662 mV, Itip = 800 pA. (b) Illustration of adsorbing model of BA II molecules.

line defects appearing as narrow threads can be found, as pointed out with white arrows in Figure 5. Most of the line

divided the rod into two equivalent parts. The statistical result gives the length of rod as 1.7 ± 0.2 nm, coinciding with the double length of BA II head parts. Hence it is reasonable to say that each single rod is composed of two BA II molecules arranging in head−head mode. However, in this mode, not enough space exists for both alkyl chains of BA II adsorbing on the surface, and two BA IIs showing as one short rod shift a certain distance from each other along the strip direction to allow interdigitation of alkyl chains in neighboring strips. In this case, the other chain could hang in the air, similar to previous publishing results on BA compounds and oligothiophene.24,27 Two BA II molecular models were overlapped in Figure 4a, and two white rectangles were used to show the shift of BA II more clearly. β, also referring to the angle between bright rod and stripe direction, is averaged as 85 ± 2°, which means the rod revolves 85° either clockwise or counter-clockwise with respect to stripes. A small shift destroys the symmetry of molecular pair leading to a chiral molecular pair, as demonstrated by the illustration in left sides of Figure 4b. In this way, mirrorreflecting domains forming with chiral molecular pair would be in nature. The unit cell of the BA II adlayer was inferred and sketched out in Figure 4a with parameters a1 = 1.0 ± 0.2 nm, a2 = 4.0 ± 0.2 nm, and α = 86 ± 2°. A tentative structure model of one kind of chiral structure was proposed on the basis of the above analysis and illustrated in Figure 4b for better understanding. In the model, only one BA II pair was given as the two hexadecyl chain (pointed out with an arrow), whereas for all other BA II molecules only the chain on surface was shown for clarification. The BA II structure is quite similar to BA derivatives studied in previous reports.24 Their assembling structure shows comparable features: head−head model with slight displacement, intercalating alkyl chain, and only one of two alkyl chains of each molecule adsorbs on surface. Dislocation caused by displacement of strips along the long axis of the bright rod can be found also, which is similar to that of BA I (image not shown here). Adsorption of BA III. In BA III (Scheme 1d), the head structure was changed to 1,3-diethyl-2-thioxodihydro-4,6pyrimidinedione compared with 2,4,6-(1H,3H)-pyrimidinetrione of BA I or BA II. Obviously interaction between BA III head parts will be much weak than that of BA I/(II) because steric hindrance of ethyl will enlarge the distance between neighbor BA III molecules. Large-scale investigation suggests that the domain size of BA III is larger but with fewer point defects or dislocations than domains of BA I and II. However,

Figure 5. Large-scale STM images of BA III adlayer. Tunneling conditions: Vbias = 577 mV, Itip = 650 pA; Inserted image: Vbias = 753 mV, Itip = 571 pA.

defects were formed near domain boundaries. The width of thin threads is about half that of the wide strips, which allows us to conclude that each wide strip has two BA III molecular rows, whereas narrow threads have only one row. 60° and 90° types of domain rotation angle can be found also, as shown in Figure 5 and inserted images, respectively. The submolecular resolution image (Figure 6a) reveals detail structure information. Short rods stack into high contrast rows with 68 ± 2° rotation angle with respect to row direction, slightly smaller compared with that of BA II structure. The rotating direction could be clockwise as the angle in Figure 6a or the inverse just as the inserted image, which leads to the formation of chiral structures. The width of bright rows is determined to be 2.1 ± 0.2 nm. Giving the width of stripes and half rows in Figure 6, we proposed that BA III adopts head− head mode on the surface with tiny shifting to allow the hexadecyl chain of BA III in neighbor strips to intercalate densely. Two BA III was superimposed in Figure 6a to show head−head arrangement. A unit cell is deduced and outlined in Figure 6a with a1 = 0.9 ± 0.2 nm, a2 = 4.5 ± 0.2 nm, and α = 70 ± 2°. On the basis of structure analysis, Figure 5b provides a tentative illustration model of BA III adlayer. In this model, two ethyl chains locating in the 1,3 position of head parts hang in air so that BA III can form a more dense structure with higher stability. Only one pair of BA III was presented as the whole 19352

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Figure 6. (a) High-resolution STM images of BA III adlayer; Tunneling conditions: Vbias = 762 mV, Itip = 749 pA; inserted image: Vbias = 753 mV, Itip = 571 pA. (b) Tentative adsorption model of BA III.

structure will help us understand assembling and membrane properties of bioactive molecules in air−water interface, solution, and real life environments, which would benefit related research such as artificial biofilm constructing, lipid molecule assembling and exchanging, vesicle forming and fusing, membrane deformation, mass transportation, and so on.

structure (marked by the black arrow in Figure 6b), whereas ethyls of all other molecules were taken for easy reading. Results show that the basic characteristics of the BA I−III adlayer are quite similar because all three molecules pair together in head−head mode, forming chiral arrangements. Assembling the structure in either two or three dimensions is a fine balance of all sorts of factors. Analysis reveals that the number of alkyl chains lying on the graphite surface for BA I− III is the same. Hence it is a reasonable explanation to attribute the assembly similarity to the resemblance of effective alkyl chain number of each molecule. When BA II adsorbs on graphite, only one chain lies on the surface, and the other one hangs in the air. Obviously, the alkyl chain in air will not affect the assembling process very much because the interaction between this kind of chain and graphite is much weaker than that of the alkyl chain directly adsorbing on surface. The similarity of the alkyl structure leading to the analogy of domain structure further implies that the structure-forming process is dominated by strong alkyl−substrate interaction. Besides the common feature, adlayers of each molecule have unique features. In the BA I adlayer, three molecular pairs group together as a unit motif. For BA III, a single molecular row can be found around the domain boundary. BA III forms head− head molecular pairs with more difficulty than BA I and BA II because sulfur-substituting and ethyl groups would weaken BAIII−BAIII intermolecular interaction greatly. However, the BA III domain structure does not change as much as expected before performing experiments and keeps the main characteristics of BA I and II arrangement surprisingly. Molecule− molecule interaction of the BA I−III system also affects the structure such as different structure motif, formation of single molecular line, and variation of molecular pair-strip angle but played only a minor role in the assembling process.

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AUTHOR INFORMATION

Corresponding Author

*Tel: +86-10-88256321. E-mail: [email protected]. Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS This work is partially supported by the President Fund of GUCAS, Starting Fund of GUCAS (grants 110300M207), and National Natural Science Foundation of China (grants 20905069 and 21003131), and the Chinese Academy of Sciences is gratefully acknowledged.

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CONCLUSIONS Adsorbing behavior of three BA derivatives with similar structure was systematically investigated with STM. Three molecules shared similar skeleton but with different numbers of alkyl chains and head−head interactions. The experiments revealed that variation of adlayer structure depends on tail parts more heavily than head parts. On the basis of analysis of molecular structure and corresponding domain features, we conclude that long alkyl chain leads to strong molecule− substrate interaction and dominates the assembly process, whereas molecule−molecule interaction forming between head parts in molecular pair is only a secondary factor. These results on relationship between assembling behavior and molecular 19353

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