Polymerization of Physisorbed Molecular Monolayers via Overhanging Alkynyl Chains: Characterization of Polymerization Kinetics and Monolayer Durability.

Monolayers self-assembled by triphenyleneethynylene (TPE) compounds bearing two terminal alkynyl chains were polymerized by Glaser-Hay (G-H) alkyne coupling at the acetonitrile-HOPG interface. The alkynyl chains extend into the solution due to the monolayer's dense-packed morphology. Reacting substructures that have no morphology-determining roles is a potential strategy for preserving monolayer morphology throughout polymerization. Monolayer G-H reaction kinetics and polymerized monolayer durability were characterized by using mass spectrometry and fluorescence. Fourier transform ion cyclotron resonance (FTICR) mass spectrometry (MS) and time-of-flight (TOF) MS were used to identify TPE-oligomers in the monolayer and to track the monolayer populations of TPE-monomer, -dimer, and -trimer as a function of G-H reaction duration. Comparison of the observed kinetics to a Monte Carlo simulation provided evidence of step-growth polymerization. The durability of polymerized monolayers depended strongly on the length of the alkynyl chains linked by G-H reaction. Polymerized T6y monolayers (O(CH2)3C≡CH alkynyl chains) desorbed minimally during 16-h immersion in 90 °C o-dichlorobenzene (oDCB), whereas polymerized T8y (O(CH2)5C≡CH alkynyl chains) and polymerized T11y (O(CH2)8C≡CH alkynyl chains), desorbed 33 and 60%, respectively, of their TPE units after 4 h in 90 °C oDCB. All the polymerized monolayers are much more durable than unpolymerized monolayers, which desorb quantitatively from HOPG when rinsed with 25 µL of oDCB. Polymerized T6y monolayer is a highly durable anchor that may be adapted to build multilayer structures "permanently" attached to the HOPG surface. The alkynyl chain length dependence may be useful for tuning polymerized TPE monolayer durability for specific applications.

Alkynyl Linkers as a Design Tool to Gain Control over the Self-Assembly of Meso-Substituted Porphyrins on HOPG.

Self-assembled monolayers (SAMs) fall generally into two broad categories: those that are covalently bound either to the surface or to each other and those that rely on weaker forces such as hydrogen bonding or van der Waals forces. The engineering of the structure of SAMs formed from weaker forces is an exciting and complex field that often utilizes long alkane substituents bound to core moieties. The core provides the unique optical, electronic, or catalytic property desired, while the interdigitation of the alkane chains provides the means for creating well-regulated patterns of cores on the substrate. This design technique sometimes fails because some of the alkane substituents remain extended into solution rather than become interdigitated on the substrate. One contributor to this is steric hindrance between elements of the core and of the alkane chain. It is shown that the use of an alkyne linker between the core and the alkane chain can, in the case of meso-substituted porphyrins, significantly reduce this steric barrier and allow more stable and predictable surface structures to form. In particular, 5,15-bis(1-octynyl)porphyrin and 5,15-bis(1-tetradecynyl)porphyrin are shown to form significantly more stable SAMs than their alkane-linked counterparts. Scanning tunneling microscopy is used to provide detailed surface structures. Temperature and solution concentration dependence of the surface coverage is also reported. Density functional theory (DFT) is used to determine the energetic effects associated with alkane substitution at both the meso and ß positions and the beneficial energetic effects of the alkyne linker.

Quantifying reversible nitrogenous ligand binding to Co(ii) porphyrin receptors at the solution/solid interface and in solution.

We present a quantitative study comparing the binding of 4-methoxypyridine, MeOPy, ligand to Co(ii)octaethylporphyrin, CoOEP, at the phenyloctane/HOPG interface and in toluene solution. Scanning tunneling microscopy (STM) was used to study the ligand binding to the porphyrin receptors adsorbed on graphite. Electronic spectroscopy was employed for examining this process in fluid solution. The on surface coordination reaction was completely reversible and followed a simple Langmuir adsorption isotherm. Ligand affinities (or ΔG) for the binding processes in the two different chemical environments were determined from the respective equilibrium constants. The free energy value of -13.0 ± 0.3 kJ mol-1 for the ligation reaction of MeOPy to CoOEP at the solution/HOPG interface is less negative than the ΔG for cobalt porphyrin complexed to the ligand in solution, -16.8 ± 0.2 kJ mol-1. This result indicates that the MeOPy-CoOEP complex is more stable in solution than on the surface. Additional thermodynamic values for the formation of the surface ligated species (ΔHc = -50 kJ mol-1 and ΔSc = -120 J mol-1) were extracted from temperature dependent STM measurements. Density functional computational methods were also employed to explore the energetics of both the solution and surface reactions. At high concentrations of MeOPy the monolayer was observed to be stripped from the surface. Computational results indicate that this is not because of a reduction in adsorption energy of the MeOPy-CoOEP complex. Nearest neighbor analysis of the MeOPy-CoOEP in the STM images revealed positive cooperative ligand binding behavior. Our studies bring new insights to the general principles of affinity and cooperativity in the ligand-receptor interactions at the solution/solid interface. Future applications of STM will pave the way for new strategies designing highly functional multisite receptor systems for sensing, catalysis, and pharmacological applications.

Balancing Noncovalent Interactions in the Self-Assembly of Nonplanar Aromatic Carboxylic Acid MOF Linkers at the Solution/Solid Interface: HOPG vs Au(111).

This study explores directed noncovalent bonding in the self-assembly of nonplanar aromatic carboxylic acids on gold and graphite surfaces. It is the first step in developing a new design strategy to create two-dimensional surface metal-organic frameworks (SURFMOFs). The acid molecules used are tetraphenylethene-based and are typically employed in the synthesis of three-dimensional (3D) MOF crystalline solids. They include tetraphenylethene tetracarboxylic acid, tetraphenylethene bisphenyl carboxylic acid, and tetraphenylethene tetrakis-phenyl carboxylic acid. The two-dimensional structures formed from these molecules on highly ordered pyrolytic graphite (HOPG) and Au(111) are studied by scanning tunneling microscopy in a solution environment. The process of monolayer formation and final surface linker structures are found to be strongly dependent on the combination of the molecule and substrate used and are discussed in terms of intermolecular and molecule-substrate interactions, bonding geometry, and symmetry of the acid molecules. In the case of linker self-assembly on HOPG, the molecule-substrate interactions play a significant role in the resulting surface structure. When the acid molecules are adsorbed on Au(111), the intermolecular interactions tend to dominate over the weaker molecule-substrate bonding. Additionally, the interplay of π-π interactions and hydrogen bonding that directs the surface self-assembly on different supports can be modified by varying the linker concentration. This is particularly applicable for the case of the acid molecules adsorbing on the Au(111) substrate. Precise control over predesigned surface structures and orientation of the nonplanar aromatic carboxylic linkers open up an exciting prospect for manipulating the direction of SURFMOF growth in two dimensions and potentially in 3D.

Cooperativity and coverage dependent molecular desorption in self-assembled monolayers: computational case study with coronene on Au(111) and HOPG.

One of the common practices in the literature of molecular desorption is the comparison of theoretically (mostly using DFT) calculated single molecule adsorption energies with experimental desorption energies from studies like temperature programmed desorption (TPD) etc. Comparisons like those do not consider that the experimental desorption energies are obtained via ensemble techniques while theoretical values are calculated at the single molecule level. Theoretical values are generally based upon desorption of a single molecule from a clean surface, or upon desorption of an entire monolayer. On the other hand, coverage dependent molecule-molecule interactions add to and modify molecule-substrate interactions that contribute to the experimentally determined desorption energies. In this work, we explore the suitability of an additive nearest neighbor model for determining general coverage dependent single molecule desorption energies in non-covalent self-assembled monolayers (SAMs). These coverage dependent values serve as essential input to any model attempting to reproduce coverage dependent desorption or for understanding the time dependent desorption from a partially covered surface. This method is tested using a case study of coronene adsorbed on Au(111) and HOPG substrates with periodic DFT calculations. Calculations show that coronene exhibits coverage and substrate dependence in molecular desorption. We found that intermolecular contact energies in the coronene monolayer are not strongly influenced by the HOPG substrate, while coronene desorption on Au(111) exhibits strong cooperativity where the additive model fails.

Kinetic and Thermodynamic Control in Porphyrin and Phthalocyanine Self-Assembled Monolayers.

Porphyrins and phthalocyanines are ubiquitous in modern science and technology. Their stability, redox properties, and photoresponse make them candidates for numerous applications. Many of these applications rely on thin films, and these are critically dependent on the first monolayer. In this article, we focus on noncovalently bound self-assembled monolayers of porphyrins and phthalocyanines at the solution-solid interface with special emphasis on the kinetic and thermodynamic processes that define the films and their reaction chemistry. We first discuss the difference between film-formation kinetics and desorption kinetics from fully formed films. We then present evidence that many of these monolayers are controlled by adsorption kinetics and are not in thermodynamic equilibrium. Measurement of the solution-solid interface desorption energy by scanning tunneling microscopy is discussed, and data is presented for cobalt, nickel, and free base octaethylporphyrin. The activation energy for the desorption of these compounds into phenyloctane is about half of the computed desorption energy in vacuum, and this is discussed in terms of the role of the solvent. Preexponential factors are very low compared to desorption into vacuum, and this is attributed to a reduction in the entropy of activation due to the participation of solvent in the transition state. An example of the use of relative desorption kinetics to create a new binary surface structure is given. It is suggested that this is a synthesis route that may have been missed because of the large difference in solution concentrations required to drive binary film formation. Attention then turns to the axial reaction chemistry of metalloporphyrins and metallophthalocyanines supported on conducting surfaces. We show several examples of chemistry unique to the supported complexes: cases where the metal binds ligands more readily and cases where the substrate induces ligand loss. Understanding this new axial coordination chemistry is of great importance in catalysis, sensing, and the growth of 3D materials from a self-assembled template.

Surface directed reversible imidazole ligation to nickel(ii) octaethylporphyrin at the solution/solid interface: a single molecule level study.

Scanning tunneling microscopy (STM) is used to study for the first time the reversible binding of imidazole (Im) and nickel(ii) octaethylporphyrin (NiOEP) supported on highly oriented pyrolytic graphite (HOPG) at the phenyloctane/NiOEP/HOPG interface at 25 °C. The ligation of Im to the NiOEP receptor while not observed in fluid solution is readily realized at the solution/HOPG interface. The coordination process scales with increasing Im concentration and can be effectively modeled by the Langmuir isotherm. At room temperature it is determined that the standard free energy of adsorption is ΔGc = -15.8 kJ mol(-1) and the standard enthalpy of adsorption is estimated to be ΔHc ≈ -80 kJ mol(-1). The reactivity of imidazole toward NiOEP adsorbed on HOPG is attributed to charge donation from the graphite stabilizing the Im-Ni bond. This charge transfer pathway is supported by molecular and periodic modeling calculations which indicate that the Im ligand behaves as a π-acceptor. DFT calculations also show that the nickel ion in the Im-NiOEP/HOPG complex is in a singlet ground state. This is surprising since both our calculations and previous experimental studies find a triplet ground state for the five and six coordinated Im-nickel(ii) porphyrins in the gas-phase or in solution. Both the experimental and the theoretical findings provide information that is useful for better understanding of chemical sensing/recognition and catalytic processes that utilize metal-organic complexes adsorbed on surfaces where the reactivity of the metal is moderated by the substrate.

A single molecule level study of the temperature-dependent kinetics for the formation of metal porphyrin monolayers on Au(111) from solution.

Scanning tunneling microscopy was used to make the first molecular scale measurements of the temperature dependence of composition of an adlayer at the solution-solid interface. We conclusively demonstrate that metal porphyrins adsorb very strongly on Au(111) at the solution solid interface such that the monolayer composition is entirely kinetically controlled below about 100 °C. The barrier for desorption is so great in fact that a temperature of 135 °C is required to induce desorption over a period of hours. Moreover, cobalt(II) octaethylporphyrin (CoOEP) and NiOEP desorb at different rates from different sites on the surface. We have measured the rate constant for desorption of CoOEP into phenyloctane to be 6.7 × 10(-5)/s at 135 °C. On the basis of these measurements, an upper bound can be set for the desorption rate of NiOEP into phenyloctane as 6.7 × 10(-4)/s at 135 °C. For solutions of the order of 100 µM in NiOEP or CoOEP, a dense monolayer is formed within seconds, and the adsorption rate constants fall within 40% of each other. The structures of NiOEP and CoOEP monolayers are essentially identical, and the molecular spacing for both can be described by A = 1.42 ± 0.02 nm, B = 1.32 ± 0.02 nm, and α = 57° ± 2°. The solubility of CoOEP and NiOEP in phenyloctane at room temperature was measured to be 0.228 and 0.319 g/L, respectively.

Effect of dispersion on surface interactions of cobalt(II) octaethylporphyrin monolayer on Au(111) and HOPG(0001) substrates: a comparative first principles study.

A density functional theory study of a cobalt(II) octaethylporphyrin (CoOEP) monolayer on Au(111) and HOPG(0001) surfaces was performed under periodic boundary conditions. Calculations with and without dispersion corrections are performed and the effect of van der Waals forces on the interface properties is analyzed. Calculations have determined that the CoOEP molecule tends to bind at the 3-fold and the 6-fold center sites on Au(111) and HOPG(0001), respectively. Geometric optimizations at the center binding sites have indicated that the porphyrin molecules (in the monolayer) lie flat on both substrates. Calculations also reveal that the CoOEP monolayer binds slightly more strongly to Au(111) than to HOPG(0001). Charge density difference plots disclose that charge is redistributed mostly around the porphyrin plane and the first layer of the substrates. Dispersion interactions cause a larger substrate to molecule charge pushback on Au(111) than on HOPG. CoOEP adsorption tends to lower the work functions of either substrate, qualitatively agreeing with the experimental photoelectron spectroscopic data. Comparison of the density of states (DOS) of the isolated CoOEP molecule with that on gold and HOPG substrates showed significant band shifts around the Fermi energy due to intermolecular orbital hybridization. Simulated STM images were plotted with the Tersoff-Hamann approach using the local density of states, which also agree with the experimental results. This study elucidates the role of dispersion for better describing porphyrin-substrate interactions. A DFT based overview of geometric, adsorption and electronic properties of a porphyrin monolayer on conductive surfaces is presented.

Thermodynamics and S-Palmitoylation Dependence of Interactions between Human Aquaporin-4 M1 Tetramers in Model Membranes.

Aquaporin-4 (AQP4) is a water channel protein found primarily in the central nervous system (CNS) that helps to regulate water-ion homeostasis. AQP4 exists in two major isoforms: M1 and M23. While both isoforms have a homotetrameric quaternary structure and are functionally identical when transporting water, the M23 isoform forms large protein aggregates known as orthogonal arrays of particles (OAPs). In contrast, the M1 isoform creates a peripheral layer around the outside of these OAPs, suggesting a thermodynamically stable interaction between the two. Structurally, the M1 isoform has an N-terminal tail that is 22 amino acids longer than the M23 isoform and contains two solvent-accessible cysteines available for S-palmitoylation at cysteine-13 (Cys-13) and cysteine-17 (Cys-17) in the amino acid sequence. Earlier work suggests that the palmitoylation of these cysteines might aid in regulating AQP4 assemblies. This work discusses the thermodynamic driving forces for M1 protein-protein interactions and how the palmitoylation state of M1 affects them. Using temperature-dependent single-particle tracking, the standard state free energies, enthalpies, and entropies were measured for these interactions. Furthermore, we present a binding model based on measured thermodynamics and a structural modeling study. The results of this study demonstrate that the M1 isoform will associate with itself according to the following expressions: 2[AQP4-M1]4 ↔ [[AQP4-M1]4]2 when palmitoylated and 3[AQP4-M1]4 ↔ [AQP4-M1]4 + [[AQP4-M1]4]2 ↔ [[AQP4-M1]4]3 when depalmitoylated. This is primarily due to a conformational change induced by adding the palmitic acid groups at Cys-13 and Cys-17 in the N-terminal tails of the homotetramers. In addition, a statistical mechanical model was developed to estimate the Gibbs free energy, enthalpy, and entropy for forming dimers and trimers. These results were in good agreement with experimental values.

Single molecule imaging of oxygenation of cobalt octaethylporphyrin at the solution/solid interface: thermodynamics from microscopy.

For the first time, the pressure and temperature dependence of a chemical reaction at the solid/solution interface is studied by scanning tunneling microscopy (STM), and thermodynamic data are derived. In particular, the STM is used to study the reversible binding of O(2) with cobalt(II) octaethylporphyrin (CoOEP) supported on highly oriented pyrolytic graphite (HOPG) at the phenyloctane/CoOEP/HOPG interface. The adsorption is shown to follow the Langmuir isotherm with P(1/2)(298K) = 3200 Torr. Over the temperature range of 10-40 °C, it was found that ΔH(P) = -68 ± 10 kJ/mol and ΔS(P) = -297 ± 30 J/(mol K). The enthalpy and entropy changes are slightly larger than expected based on solution-phase reactions, and possible origins of these differences are discussed. The big surprise here is the presence of any O(2) binding at room temperature, since CoOEP is not expected to bind O(2) in fluid solution. The stability of the bound oxygen is attributed to charge donation from the graphite substrate to the cobalt, thereby stabilizing the polarized Co-O(2) bonding. We report the surface unit cell for CoOEP on HOPG in phenyloctane at 25 °C to be A = (1.46 ± 0.1)n nm, B = (1.36 ± 0.1)m nm, and α = 54 ± 3°, where n and m are unknown nonzero non-negative integers.

Tunneling spectroscopy of organic monolayers and single molecules.

Basic concepts in tunneling spectroscopy applied to molecular systems are presented. Junctions of the form M-A-M, M-I-A-M, and M-I-A-I'-M, where A is an active molecular layer, are considered. Inelastic electron tunneling spectroscopy (IETS) is found to be readily applied to all the above device types. It can provide both vibrational and electron spectroscopic data about the molecules comprising the A layer. In IETS there are no strong selection rules (although there are preferences) so that transitions that are normally IR, Raman, or even photon-forbidden can be observed. In the electronic transition domain, spin and Laporte forbidden transitions may be observed. Both vibrational and electronic IETS can be acquired from single molecules. The negative aspect of this seemingly ideal spectroscopic method is the thermal line width of about 5 k(B)T. This limits the useful measurement of vibrational IETS to temperatures below about 10 K. In the case of most electronic transitions where the intrinsic linewidth is much broader, useful experiments above 100 K are possible. One further limitation of electronic IETS is that it is generally limited to transitions with energy less than about 20,000 cm(-1). IETS can be identified by peaks in d(2) I/dV (2) vs bias voltage plots that occur at the same position (but not necessarily same intensity) in either bias polarity.Elastic tunneling spectroscopy is discussed in the context of processes involving molecular ionization and electron affinity states, a technique we call orbital mediated tunneling spectroscopy, or OMTS. OMTS can be applied readily to M-I-A-M and M-I-A-I'-M systems, but application to M-A-M junctions is problematic. Spectra can be obtained from single molecules. Ionization state results correlate well with UPS spectra obtained from the same systems in the same environment. Both ionization and affinity levels measured by OMTS can usually be correlated with one electron oxidation and reduction potentials for the molecular species in solution. OMTS can be identified by peaks in dI/dV vs bias voltage plots that do not occur at the same position in either bias polarity. Because of the intrinsic width of the ionization and affinity transitions, OMTS can be applied at temperatures above 500 K.This is not a comprehensive review of more than 20 years of research and there are many excellent papers that are not cited here. An absence of a citation is not a reflection on the quality of the work.

Fabrication of graphene with CuO islands by chemical vapor deposition.

Graphene prepared on Cu foil by chemical vapor deposition was studied as a function of post growth cooling conditions. CuO islands embedded in the graphene film were discovered and studied by scanning electron microscopy, atomic force microscopy, and X-ray photoemission spectroscopy. It is shown that nanostructured holes can be formed within a graphene film by reduction using hydrogen cooling immediately after film growth. We also observe the formation of symmetrical oxide islands in these holes. This study provides an easy way to fabricate a graphene + CuO composite, and the method may be extended to other graphene based structures.

Single-Molecule Kinetic Analysis of Oxygenation of Co(II) Porphyrin at the Solution/Solid Interface.

Kinetic analysis of surface reactions at the single molecule level is important for understanding the influence of the substrate and solvent on reaction dynamics and mechanisms, but it is difficult with current methods. Here we present a stochastic kinetic analysis of the oxygenation of cobalt octaethylporphyrin (CoOEP) at the solution/solid interface by monitoring fluctuations from equilibrium using scanning tunneling microscopy (STM) imaging. Image movies were used to monitor the oxygenated and deoxygenated state dwell times. The rate constants for CoOEP oxygenation are ka = 4.9 × 10-6 s-1·Torr-1 and kd = 0.018 s-1. This is the first use of stochastic dwell time analysis with STM to study a chemical reaction, and the results suggest that it has great potential for application to a wide range of surface reactions. Expanding these stochastic studies to further systems is key to unlocking kinetic information for surface-confined reactions at the molecular level, especially at the solution/solid interface.

Differing HOMO and LUMO mediated conduction in a porphyrin nanorod.

In this communication we provide the first UHV-STM images and STM-based current-voltage (I-V) and orbital mediated tunneling spectroscopy (OMTS) data on a self-assembled porphyrin nanostructure at the single structure level. We will show that transverse conductivity over distances less than 10 nm can occur by barrier type tunneling but that long distance conduction solely occurs through the LUMO band. These nanorods are very highly rectifying.

Building self-assembled molecular layers with axially substituted titanium phthalocyanines.

Adsorption on graphite (HOPG) by titanium phthalocyanine axially bonded to a catechol ligand (TiPcat), titanylphthalocyanine (TiOPc), and 1:1 mixtures of these are studied at the HOPG-octylbenzene interface. The surface structures of a two-component bilayer, and of the individual monolayers of TiOPc and TiPcat, were determined by scanning tunneling microscopy (STM). TiPcat self-segregates onto a monolayer of TiOPc when an equal molar mixture is used. The preferential formation of a TiOPc monolayer from a solution containing both molecules is attributed to the difference in adsorption energies between TiPcat and TiOPc on graphite. The transformation of the hexagonal lattice of the pure TiOPc monolayer into a pseudo-square lattice was induced by the adsorption of TiPcat molecules. DFT calculations of the catechol orientation are presented.

Molecular electronics. It's all about contacts.

A key requirement in molecular electronics studies is the ability to measure the conductivity of a single molecule. But as Hipps explains in his Perspective, such measurements are often more about contacts than about molecular conductivity. Depending on the experimental setup, DNA behaves like a semiconductor, insulator, or metal. Cui et al. have designed a method that overcomes some of these problems, opening the door to systematic, reliable, and reproducible studies of the molecule-contact interface.

Kinetic and thermodynamic processes of organic species at the solution-solid interface: the view through an STM.

A focused review is presented on the evolution of our understanding of the kinetic and thermodynamic factors that play a critical role in the formation of well ordered organic adlayers at the solution-solid interface. While the current state of knowledge is in the very early stages, it is now clear that assumptions of kinetic or thermodynamic control are dangerous and require careful confirmation. Equilibrium processes at the solution-solid interface are being described by evolving thermodynamic models that utilize concepts from the thermodynamics of micelles. A surface adsorption version of the Born-Haber cycle is helping to extract the thermodynamic functions of state associated with equilibrium structures, but only a very few systems have been so analyzed. The kinetics of surface phase transformation, especially for polymorphic phases is in an early qualitative stage. Adsorption and desorption kinetics are just starting to be measured. The study of kinetics and thermodynamics for organic self-assembly at the solution-solid interface is experiencing very exciting and rapid growth.

Hyperbranched crystalline nanostructure produced from ionic π-conjugated molecules.

Self-assembled crystalline nanostructures with sheaf-like morphology fabricated from tetra(4-aminophenyl)porphyrin and tetra(4-sulfonatophenyl)porphyrin are reported for the first time. The hierarchical sheaf-like growth of the assemblies exhibits Arrhenius behaviour. The observed morphology results from crystal splitting during initial oriented attachment growth followed by Ostwald ripening.

Intrinsically disordered protein.

Proteins can exist in a trinity of structures: the ordered state, the molten globule, and the random coil. The five following examples suggest that native protein structure can correspond to any of the three states (not just the ordered state) and that protein function can arise from any of the three states and their transitions. (1) In a process that likely mimics infection, fd phage converts from the ordered into the disordered molten globular state. (2) Nucleosome hyperacetylation is crucial to DNA replication and transcription; this chemical modification greatly increases the net negative charge of the nucleosome core particle. We propose that the increased charge imbalance promotes its conversion to a much less rigid form. (3) Clusterin contains an ordered domain and also a native molten globular region. The molten globular domain likely functions as a proteinaceous detergent for cell remodeling and removal of apoptotic debris. (4) In a critical signaling event, a helix in calcineurin becomes bound and surrounded by calmodulin, thereby turning on calcineurin's serine/threonine phosphatase activity. Locating the calcineurin helix within a region of disorder is essential for enabling calmodulin to surround its target upon binding. (5) Calsequestrin regulates calcium levels in the sarcoplasmic reticulum by binding approximately 50 ions/molecule. Disordered polyanion tails at the carboxy terminus bind many of these calcium ions, perhaps without adopting a unique structure. In addition to these examples, we will discuss 16 more proteins with native disorder. These disordered regions include molecular recognition domains, protein folding inhibitors, flexible linkers, entropic springs, entropic clocks, and entropic bristles. Motivated by such examples of intrinsic disorder, we are studying the relationships between amino acid sequence and order/disorder, and from this information we are predicting intrinsic order/disorder from amino acid sequence. The sequence-structure relationships indicate that disorder is an encoded property, and the predictions strongly suggest that proteins in nature are much richer in intrinsic disorder than are those in the Protein Data Bank. Recent predictions on 29 genomes indicate that proteins from eucaryotes apparently have more intrinsic disorder than those from either bacteria or archaea, with typically > 30% of eucaryotic proteins having disordered regions of length > or = 50 consecutive residues.