Journal of the American Chemical Society Figure 1. (a) Molecular structures of the terpyrimidinethiols ([2,50:20, 500-terpyrimidine]-200-thiol, 3Ndown, and [2,50:20,500-terpyrimidine]-5-thiol, 3Nup), unsubstituted terpyrimidine (3N), and terphenyl (3P). The perma- nent dipole moments of the pyrimidines are indicated by black arrows (direction deﬁned as pointing from negative to positive charge). (b) Top view of the investigated monolayers in the (√3 3) surface unit-cell. The Cartesian axes are indicated. a priori unexpected features, whose discussion and explanation provide interesting new insights into eﬀects that can be exploited to alter the electronic structure of SAMs, especially when they are made of oligomers with polar repeat units. These are brieﬂy outlined in the following: I. As mentioned above, tail-group substitutions in many cases33,41 change the molecular eigenenergies but do not impact the level alignment at a metal/organic interface. We ﬁnd that the exact opposite is true for 3Nup and 3Ndown gold/monolayer systems: The frontier molecular orbital energies for 3Nup and 3Ndown molecules are essentially identical, whereas for 3Nup and 3Ndown monolayers the alignment of the electronic states with the gold Fermi-level is totally diﬀerent.44 II. External ﬁelds have been shown to modify orbital (band) energies, the frontier orbital (band) gap, and the ener- getic ordering of the electronic states in molecules and monolayers;45 54 related mechanisms have recently been suggested also for inorganic cluster assemblies.55 The ﬁeld distorts and localizes eigenstates,53,54 and recent studies imply that such processes are relevant also when the ﬁeld originates from dipoles embedded within the layer,34 result- ing in a shift in the optical absorption spectrum.45,46 Internally generated electric ﬁelds can be expected to be at work also in pyrimidine-based SAMs, as every pyrimidine unit carries an electric dipole moment. In contrast to tail-group substituted SAMs, where the resulting poten- tial gradient is conﬁned essentially to the substituent region,56,42,33 the distributed dipoles in an oligopyromidine SAM give rise to a potential gradient throughout the entire monolayer. The associated eﬀective internal ﬁelds are comparably large (in the range of 107 V/cm), which makes ARTICLE oligopyrimidines an ideal test-bed for studying their impact on the electronic structure of a SAM. This aspect, to the best of our knowledge, has not yet been studied systematically. III. Upon increasing the SAM packing density and thereby the electric ﬁeld, the molecular dipoles depolarize each other. Such (de)polarization eﬀects in SAMs arising from internal31,56,57 as well as external58,59,56 electric ﬁelds have been the topic of several studies. Here we explain why, in spite of the depolarization of the overall charge density, the collectively generated ﬁeld polarizes rather than depo- larizes the electron densities associated with the frontier orbitals. In addressing the above aspects, we establish a microscopic understanding of the relevant physicochemical processes in SAMs of molecules consisting of repeated dipolar building blocks. In particular, we describe collective eﬀects that strongly modify SAM properties and, thus, need to be considered in “molecular design” approaches and their optimization. Prior to discussing the electronic structure of the oligopyrimidine layers, it is, however, necessary to provide some details on the chosen model system and also to clarify an important methodological issue that arises from the use of density-functional theory (DFT). The latter is essential, as DFT is the only approach allowing for a realistic, fully quantum-mechanical treatment of two-dimen- sional periodic arrangements of the size explored here. ’ RESULTS AND DISCUSSION System. The focus of the present contribution is on processes within the molecular monolayer. Therefore, as a first step we avoid effects involving the interaction with a metallic substrate by excluding the metal from most of our calculations. This is insofar justified as numerous studies have found that the bonding- induced charge rearrangements are confined to the very vicinity of the docking groups,60,61 unless so-called Fermi-level pinning occurs.62 Such charge rearrangements should, thus, have only a minor effect on the field distribution within the SAM, which is crucial for the effects discussed in this paper. Moreover, in densely packed monolayers the collectively induced electric field acting within the monolayer virtually does not extend onto the metal for electrostatic reasons, as its decay length amounts to only roughly one-sixth of the interdipole distance.42 The docking chemistry and the interaction with the metal, however, directly affect the order of σ- and π-states. This is addressed later in the paper. In ref 44, where certain properties of the bonded monolayer are discussed, a herringbone arrangement of the oligopyrimidi- nethiols in the (√3 3) Au(111) surface unit-cell has been assumed. This is a plausible choice, as it has been reported that the related biphenylthiols arrange in this way on Au(111).63 In fact, oligophenylenes generally tend to crystallize in the herring- bone pattern,64 and this might hold true also for longer oligopyr- imidinethiols. At least for monopyrimidinethiols, however, this appears not to be the case: For them, a mixed structure of ﬂat lying and upright standing molecules in larger unit cells has been reported.65,66 The situation is further complicated by the ob- servation that for substituted monopyrimidinethiols the mol- ecules were found to arrange in parallel rows at an even less dense packing.67 As we are not aware of a work in which assemblies of unsubstituted oligopyrimidinethiols of the type shown in Figure 1 have been studied, it is a plausible compromise to consider such 18635 dx.doi.org/10.1021/ja203579c |J. Am. Chem. Soc. 2011, 133, 18634–18645