Showing papers in "Annual Review of Physical Chemistry in 2012"
TL;DR: Energy gap matching for reduction of CO(2) to different products, including CO, formic acid, and methanol, is used to identify the most promising systems.
Abstract: The recent literature on photochemical and photoelectrochemical reductions of CO(2) is reviewed. The different methods of achieving light absorption, electron-hole separation, and electrochemical reduction of CO(2) are considered. Energy gap matching for reduction of CO(2) to different products, including CO, formic acid, and methanol, is used to identify the most promising systems. Different approaches to lowering overpotentials and achieving high chemical selectivities by employing catalysts are described and compared.
928 citations
TL;DR: To characterize structure or structural changes, experimental protocols were optimized and techniques for artifact suppression were introduced, and it was realized that interpretation of the distance distributions must take into account the conformational distribution of spin labels.
Abstract: Distance distributions between paramagnetic centers in the range of 1.8 to 6 nm in membrane proteins and up to 10 nm in deuterated soluble proteins can be measured by the DEER technique. The number of paramagnetic centers and their relative orientation can be characterized. DEER does not require crystallization and is not limited with respect to the size of the protein or protein complex. Diamagnetic proteins are accessible by site-directed spin labeling. To characterize structure or structural changes, experimental protocols were optimized and techniques for artifact suppression were introduced. Data analysis programs were developed, and it was realized that interpretation of the distance distributions must take into account the conformational distribution of spin labels. First methods have appeared for deriving structural models from a small number of distance constraints. The present scope and limitations of the technique are illustrated.
821 citations
TL;DR: The objective of this article is to continue where a previous review of TD-DFT in Volume 55 of the Annual Review of Physical Chemistry left off and highlight some of the problems and solutions from the point of view of applied physical chemistry.
Abstract: The classic density-functional theory (DFT) formalism introduced by Hohenberg, Kohn, and Sham in the mid-1960s is based on the idea that the complicated N-electron wave function can be replaced with the mathematically simpler 1-electron charge density in electronic structure calculations of the ground stationary state. As such, ordinary DFT cannot treat time-dependent (TD) problems nor describe excited electronic states. In 1984, Runge and Gross proved a theorem making TD-DFT formally exact. Information about electronic excited states may be obtained from this theory through the linear response (LR) theory formalism. Beginning in the mid-1990s, LR-TD-DFT became increasingly popular for calculating absorption and other spectra of medium- and large-sized molecules. Its ease of use and relatively good accuracy has now brought LR-TD-DFT to the forefront for this type of application. As the number and the diversity of applications of TD-DFT have grown, so too has our understanding of the strengths and weakness...
683 citations
TL;DR: A general overview of the field of single-molecule (SM) surface-enhanced Raman spectroscopy (SERS) as it stands today is provided and some of the latest developments and promising new leads are presented.
Abstract: A general overview of the field of single-molecule (SM) surface-enhanced Raman spectroscopy (SERS) as it stands today is provided. After years of debates on the basic aspects of SM-SERS, the technique is emerging as a well-established subfield of spectroscopy and SERS. SM-SERS is allowing the observation of subtle spectroscopic phenomena that were not hitherto accessible. Examples of the latter are natural isotopic substitutions in single molecules, observation of the true homogeneous broadening of Raman peaks, Raman excitation profiles of individual molecules, and SM electrochemistry. With background examples of the contributions produced by our group, properly interleaved with results by other practitioners in the field, we present some of the latest developments and promising new leads in this new field of spectroscopy.
645 citations
TL;DR: The thiol-induced blinking of Cy5, a curse for single-molecule biophysical studies that was later overcome using Trolox through a reducing/oxidizing system but a boon for super-resolution imaging owing to the controllable photoswitching, is reviewed.
Abstract: Single-molecule fluorescence spectroscopy and super-resolution microscopy are important elements of the ongoing technical revolution to reveal biochemical and cellular processes in unprecedented clarity and precision. Demands placed on the photophysical properties of the fluorophores are stringent and drive the choice of appropriate probes. Such fluorophores are not simple light bulbs of a certain color and brightness but instead have their own “personalities” regarding spectroscopic parameters, redox properties, size, water solubility, photostability, and several other factors. Here, we review the photophysics of fluorescent probes, both organic fluorophores and fluorescent proteins, used in applications such as particle tracking, single-molecule FRET, stoichiometry determination, and super-resolution imaging. Of particular interest is the thiol-induced blinking of Cy5, a curse for single-molecule biophysical studies that was later overcome using Trolox through a reducing/oxidizing system but a boon for ...
596 citations
TL;DR: This review describes how conical intersections affect measured molecular spectra and simple photofragmentation processes, and considers excitations that result in electron ejection or photodetachment, as well as photoinduced H-atom elimination.
Abstract: This review describes how conical intersections affect measured molecular spectra and simple photofragmentation processes. We consider excitations that result in electron ejection, that is, photoionization or photodetachment, as well as photoinduced H-atom elimination. Section 1 presents a brief overview of the history of conical intersections and their rise from an arcane theoretical concept to a major paradigm in nonadiabatic chemistry. In Section 2, the generic properties of conical intersections are discussed, as well as their characterization with modern electronic-structure methods. Section 3 briefly discusses computational tools used to compute the nuclear motion involving conical intersections. Section 4 describes how the ideas of Sections 2 and 3 are combined to simulate molecular spectra impacted by conical intersections. Section 5 describes selected recent experimental and computational studies of photoelectron, photodetachment, and photofragment spectra. Rather than providing an encyclopedic bibliography of the previous and current literature, we illustrate significant problems currently being addressed and describe what can be accomplished with current computational techniques and how these results are achieved. Section 6 suggests future directions in this field.
404 citations
TL;DR: This review provides both traditional and new examples of Relativistic effects, including the special properties of gold, lead-acid and mercury batteries, the shapes of gold and thallium clusters, heavy-atom shifts in NMR, topological insulators, and certain specific heats.
Abstract: Relativistic effects can strongly influence the chemical and physical properties of heavy elements and their compounds. This influence has been noted in inorganic chemistry textbooks for a couple of decades. This review provides both traditional and new examples of these effects, including the special properties of gold, lead-acid and mercury batteries, the shapes of gold and thallium clusters, heavy-atom shifts in NMR, topological insulators, and certain specific heats.
403 citations
TL;DR: In this review, TERS enhancements are discussed in some detail, including a condensed overview of measured contrasts and estimated total enhancements.
Abstract: Tip-enhanced Raman spectroscopy (TERS) is a very powerful variant of surface-enhanced Raman spectroscopy (SERS). In a sense, TERS overcomes most of the drawbacks of SERS but keeps its advantages, such as its high sensitivity. TERS offers the additional advantages of high spatial resolution, much beyond the Abbe limit, and the possibility to correlate TER and other scanning probe microscope images, i.e., to correlate topographic and chemical data. TERS finds application in a number of fields, such as surface science, material science, and biology. Single-molecule TERS has been observed even for TERS enhancements of “only” 10 6 –10 7 . In this review, TERS enhancements are discussed in some detail, including a condensed overview of measured contrasts and estimated total enhancements. Finally, recent developments for TERS under ultrahigh vacuum conditions are presented, including TERS on a C60 island with a diameter of a few tens of nanometers, deposited on a smooth Au(111) surface.
277 citations
TL;DR: Synthetic fluorophores have a small size, are available in many colors spanning the whole spectrum, and can easily be chemically modified and used for stoichiometric labeling of proteins in live cells.
Abstract: Super-resolution imaging methods now can provide spatial resolution that is well below the diffraction limit approaching virtually molecular resolution. They can be applied to biological samples and provide new and exciting views on the structural organization of cells and the dynamics of biomolecular assemblies on wide timescales. These revolutionary developments come with novel requirements for fluorescent probes, labeling techniques, and data interpretation strategies. Synthetic fluorophores have a small size, are available in many colors spanning the whole spectrum, and can easily be chemically modified and used for stoichiometric labeling of proteins in live cells. Because of their brightness, their photostability, and their ability to be operated as photoswitchable fluorophores even in living cells under physiological conditions, synthetic fluorophores have the potential to substantially accelerate the broad application of live-cell super-resolution imaging methods.
248 citations
TL;DR: A brief history of microgel-based colloidal dispersions is reviewed and their transition from tunable hard spheres to a class of soft matter that has revealed a landscape of physics and chemistry notable for its extraordinary richness and diversity is discussed.
Abstract: Colloidal dispersions have been studied for decades as a result of their utility in numerous applications and as models for molecular and atomic condensed phases. More recently, a number of groups have exploited in such studies submicrometer-sized hydrogel particles (microgels) that have environmentally tunable sizes. The experimental convenience of tuning the dispersion's colloidal volume fraction while maintaining a constant number density of particles provides a clear advantage over more tedious studies that employ traditional hard-sphere particles. However, as studies delved deeper into the fundamental physics of colloidal dispersions comprising microgel particles, it became abundantly clear that a microgel's utility as a tunable hard sphere was limited and that the impact of softness was more profound than previously appreciated. Herein we review the brief history of microgel-based colloidal dispersions and discuss their transition from tunable hard spheres to a class of soft matter that has revealed a landscape of physics and chemistry notable for its extraordinary richness and diversity.
226 citations
TL;DR: Recent developments of nonlinear light scattering techniques have resulted in a deeper insight of the underlying light-matter interactions and shed new light on the molecular mechanism of surface kinetics in solution, properties of interfacial water in contact with hydrophilic and hydrophobic particles and droplets, and vesicle structure and transport properties.
Abstract: Nano- and microparticles have optical, structural, and chemical properties that differ from both their building blocks and the bulk materials themselves. These different physical and chemical properties are induced by the high surface-to-volume ratio. As a logical consequence, to understand the properties of nano- and microparticles, it is of fundamental importance to characterize the particle surfaces and their interactions with the surrounding medium. Recent developments of nonlinear light scattering techniques have resulted in a deeper insight of the underlying light-matter interactions. They have shed new light on the molecular mechanism of surface kinetics in solution, properties of interfacial water in contact with hydrophilic and hydrophobic particles and droplets, molecular orientation distribution of molecules at particle surfaces in solution, interfacial structure of surfactants at droplet interfaces, acid-base chemistry on particles in solution, and vesicle structure and transport properties.
TL;DR: The first ten years of attosecond science is reviewed with a selection of recent highlights and trends, and the main spectroscopic tools are introduced and recent examples of representative experiments employing them are given.
Abstract: We review the first ten years of attosecond science with a selection of recent highlights and trends and give an outlook on future directions. After introducing the main spectroscopic tools, we give recent examples of representative experiments employing them. Some of the most fundamental processes in nature have been studied with some results initiating controversial discussions. Experiments on the dynamics of single-photon ionization illustrate the importance of subtle effects on such extreme timescales and lead us to question some of the well-established assumptions in this field. Attosecond transient absorption, as the first all-optical approach to resolve attosecond dynamics, has been used to study electron wave packet interferences in helium. The attoclock, a recent method providing attosecond time resolution without the explicit need for attosecond pulses, has been used to investigate electron tunneling dynamics and geometry. Pushing the frontiers in attosecond quantum mechanics with increasing temporal and spatial resolution and often limited theoretical models results in unexpected observations. At the same time, attosecond science continues to expand into more complex solid-state and molecular systems, where it starts to have impact beyond its traditional grounds.
TL;DR: This review covers how nuclear singlet states may be generated, observed, and exploited in solution nuclear magnetic resonance (NMR) and potential applications include the study of slow molecular processes, the elucidation of molecular geometry, and the transport of hyperpolarized nuclear spin order.
Abstract: Nuclear singlet states may have lifetimes that are much longer than the conventional relaxation time of nuclear spin magnetization. This review covers how these states may be generated, observed, and exploited in solution nuclear magnetic resonance (NMR). Potential applications include the study of slow molecular processes, the elucidation of molecular geometry, and the transport of hyperpolarized nuclear spin order.
TL;DR: Comparison of the solid-state and solution NMR structures provides important insights into the effects of the solubilizing environment on membrane protein structure and dynamics.
Abstract: We review the current state of membrane protein structure determination using solid-state nuclear magnetic resonance (NMR) spectroscopy. Multidimensional magic-angle-spinning correlation NMR combined with oriented-sample experiments has made it possible to measure a full panel of structural constraints of membrane proteins directly in lipid bilayers. These constraints include torsion angles, interatomic distances, oligomeric structure, protein dynamics, ligand structure and dynamics, and protein orientation and depth of insertion in the lipid bilayer. Using solid-state NMR, researchers have studied potassium channels, proton channels, Ca(2+) pumps, G protein-coupled receptors, bacterial outer membrane proteins, and viral fusion proteins to elucidate their mechanisms of action. Many of these membrane proteins have also been investigated in detergent micelles using solution NMR. Comparison of the solid-state and solution NMR structures provides important insights into the effects of the solubilizing environment on membrane protein structure and dynamics.
TL;DR: This review intends to provide a first overview on upcoming possibilities, emerging technologies, pioneering results, and future perspectives in this exciting field of free-electron lasers.
Abstract: Free-electron lasers are fourth-generation light sources that deliver extremely intense (>1012 photons per pulse), ultrashort (∼10−14 s = 10 fs) light pulses at up to kilohertz repetition rates with unprecedented coherence properties and span a broad wavelength regime from soft (∼10 eV) to hard X-ray energies (∼15 keV). They thus enable a whole suite of novel experiments in molecular physics and chemistry: Inspecting radiation-induced reactions in cold molecular ions provides unprecedented insight into the photochemistry of interstellar clouds and upper planetary atmospheres; double core-hole photoelectron spectroscopy offers enhanced sensitivity for chemical analysis; the dynamics of highly excited molecular states, pumped by vacuum ultraviolet pulses, can be inspected; and vacuum ultraviolet or X-ray probe pulses generally hold the promise to trace chemical reactions along an entire reaction coordinate with atomic spatial and temporal resolution. This review intends to provide a first overview on upcomi...
TL;DR: The application of vibrational sum frequency generation (VSFG), an inherently surface-specific, even-order nonlinear optical spectroscopy, enables the direct interrogation of various vapor/aqueous interfaces to elucidate the behavior and reaction of chemical species within the surface regime.
Abstract: The chemistry that occurs at surfaces has been an intense area of study for many years owing to its complexity and importance in describing a wide range of physical phenomena. The vapor/water interface is particularly interesting from an environmental chemistry perspective as this surface plays host to a wide range of chemistries that influence atmospheric and geochemical interactions. The application of vibrational sum frequency generation (VSFG), an inherently surface-specific, even-order nonlinear optical spectroscopy, enables the direct interrogation of various vapor/aqueous interfaces to elucidate the behavior and reaction of chemical species within the surface regime. In this review we discuss the application of VSFG to the study of a variety of atmospherically important systems at the vapor/aqueous interface. Chemical systems presented include inorganic ionic solutions prevalent in aqueous marine aerosols, small molecular solutes, and long-chain fatty acids relevant to fat-coated aerosols. The ability of VSFG to probe both the organization and reactions that may occur for these systems is highlighted. A future perspective toward the application of VSFG to the study of environmental interfaces is also provided.
TL;DR: Recent insights into the structure and thermodynamics of confined water that have been elucidated primarily by computer simulation studies are reviewed.
Abstract: The behavior of water confined on nanometer length scales is important in a diverse set of technical and scientific contexts, ranging from the performance of fuel cells and biological molecular machines to the design of self-assembling nanoscale materials. Here, we review recent insights into the structure and thermodynamics of confined water that have been elucidated primarily by computer simulation studies. We emphasize investigations in which interfacial chemistry and molecular topography are varied systematically and in which a wide range of thermodynamic conditions of temperature and pressure are explored. We consider homogeneous interfaces ranging from the simplest hard wall to chemically realistic, but structurally ideal, hydrophobic and hydrophilic surfaces, and the continuous scale of surface polarity is investigated. Features associated with interface heterogeneities arising from chemical patterning or from the natural characteristics of protein surfaces are discussed. Finally, we provide our thoughts on important directions for further studies.
TL;DR: In this review, phenomena specifically connected to ultrathin oxide films are discussed to explain and understand the physicochemical basis of their reactivity in oxidation reactions.
Abstract: Well-ordered, thin oxide films have drawn some attention in recent years as suitable oxide supports for modeling highly dispersed metal catalysts at the atomic scale. It turned out, however, that ultrathin oxide films may exhibit interesting catalytic properties in their own right. In this review, we discuss phenomena specifically connected to ultrathin oxide films to explain and understand the physicochemical basis of their reactivity in oxidation reactions. Two sets of systems are discussed, i.e., transition metal oxide films grown on metal substrates and native oxide films formed upon oxidation of metal surfaces.
TL;DR: Recent developments in the behavior of halide salts at the vapor/water interface are discussed, based on classical and quantum-chemical molecular simulations as well as developments that are based on simple potential models.
Abstract: The behavior of halide salts at the vapor/water interface has been the focus of a tremendous amount of work in the past ten years. A molecular view of the interface has been introduced with the observation that large anions have some affinity for the interface, but a quantitative description of the driving forces that determine ion adsorption or repulsion at the interface is still missing. This review discusses recent developments that are based on classical and quantum-chemical molecular simulations as well as developments that are based on simple potential models.
TL;DR: In this article, the authors present a review of recoupling techniques in SSNMR and recall the major steps achieved by the community throughout the last two decades and discuss their implications regarding dipolar truncation and the possibility to extract structural data in the spectra.
Abstract: Solid-state nuclear magnetic resonance (SSNMR) magic angle spinning (MAS) can be used to record high-resolution data dominated by site-specific information. Although MAS introduces high resolution by attenuating the anisotropic broadening, it also suppresses the nuclear dipole-dipole distance information that is the source of most structural data in the spectra. Such information can be reintroduced coherently and thus selectively by the application of a carefully chosen sequence of radiofrequency pulses, an approach that was introduced 20 years ago and is referred to as dipolar recoupling. This review presents the establishment of recoupling techniques in SSNMR and recalls the major steps achieved by the community throughout the last two decades. This review also presents emerging techniques and their corresponding new concepts. Finally, we present some recent developments based on second-order recoupling mechanisms and discuss their implications regarding dipolar truncation and the possibility to extract...
TL;DR: By combining surface-science characterization methods with kinetic measurements under realistic working conditions, researchers are continuing to advance the molecular-level understanding of heterogeneous catalysis and are narrowing the pressure and material gap between model and real-world catalysts.
Abstract: Surface-science investigations have contributed significantly to heterogeneous catalysis in the past several decades. Fundamental studies of reactive systems on metal single crystals have aided researchers in understanding the effect of surface structure on catalyst reactivity and selectivity for a number of important reactions. Recently, model systems, consisting of metal clusters deposited on planar oxide surfaces, have facilitated the study of metal particle-size and support effects. These model systems not only are useful for carrying out kinetic investigations, but are also amenable to surface spectroscopic techniques, thus enabling investigations under realistic pressures and at working temperatures. By combining surface-science characterization methods with kinetic measurements under realistic working conditions, researchers are continuing to advance the molecular-level understanding of heterogeneous catalysis and are narrowing the pressure and material gap between model and real-world catalysts.
TL;DR: These instruments can now provide real-time, size-resolved aerosol particle physical property and chemical composition data anywhere in Earth's troposphere and lower stratosphere.
Abstract: For more than two decades a cadre of physical chemists has focused on understanding the formation processes, chemical composition, and chemical kinetics of atmospheric aerosol particles and droplets with diameters ranging from a few nanometers to ∼10,000 nm. They have adapted or invented a range of fundamental experimental and theoretical tools to investigate the thermochemistry, mass transport, and chemical kinetics of processes occurring at nanoscale gas-liquid and gas-solid interfaces for a wide range of nonideal, real-world substances. State-of-the-art laboratory methods devised to study molecular spectroscopy, chemical kinetics, and molecular dynamics also have been incorporated into field measurement instruments that are deployed routinely on research aircraft, ships, and mobile laboratories as well as at field sites from megacities to the most remote jungle, desert, and polar locations. These instruments can now provide real-time, size-resolved aerosol particle physical property and chemical composition data anywhere in Earth's troposphere and lower stratosphere.
TL;DR: This review summarizes recent research progress in understanding neurotrophin-receptor interactions at the axonal terminal and their transport dynamics along the axon and emphasizes high-resolution studies at the single-molecule level.
Abstract: Neurotrophins are a family of target-derived growth factors that support survival, development, and maintenance of innervating neurons. Owing to the unique architecture of neurons, neurotrophins that act locally on the axonal terminals must convey their signals across the entire axon for subsequent regulation of gene transcription in the cell nucleus. This long-distance retrograde signaling, a motor-driven process that can take hours or days, has been a subject of intense interest. In the last decade, live-cell imaging with high sensitivity has significantly increased our capability to track the transport of neurotrophins, their receptors, and subsequent signals in real time. This review summarizes recent research progress in understanding neurotrophin-receptor interactions at the axonal terminal and their transport dynamics along the axon. We emphasize high-resolution studies at the single-molecule level and also discuss recent technical advances in the field.
TL;DR: Together theoretical and experimental developments have broadened understanding of isotope effects and extended the range of chemical systems where these unique effects occur and furthered the understanding of events such as solar system origin and evolution and planetary atmospheric chemistry, present and past.
Abstract: Historically, the physical chemistry of isotope effects and precise measurements in samples from nature have provided information on processes that could not have been obtained otherwise. With the discovery of a mass-independent isotopic fractionation during the formation of ozone, a new physical chemical basis for isotope effects required development. Combined theoretical and experimental developments have broadened this understanding and extended the range of chemical systems where these unique effects occur. Simultaneously, the application of mass-independent isotopic measurements to an extensive range of both terrestrial and extraterrestrial systems has furthered the understanding of events such as solar system origin and evolution and planetary atmospheric chemistry, present and past.
TL;DR: Two correlated cellular imaging techniques are reviewed that fulfill the need for detailed knowledge of both the subcellular architecture and the location of specific molecules within this framework and can be applied across the spectrum of problems encountered in cell biology.
Abstract: Living cells are structured to create a range of microenvironments that support specific chemical reactions and processes. Understanding how cells function therefore requires detailed knowledge of both the subcellular architecture and the location of specific molecules within this framework. Here we review the development of two correlated cellular imaging techniques that fulfill this need. Cells are first imaged using cryogenic fluorescence microscopy to determine the location of molecules of interest that have been labeled with fluorescent tags. The same specimen is then imaged using soft X-ray tomography to generate a high-contrast, 3D reconstruction of the cells. Data from the two modalities are then combined to produce a composite, information-rich view of the cell. This correlated imaging approach can be applied across the spectrum of problems encountered in cell biology, from basic research to biotechnological and biomedical applications such as the optimization of biofuels and the development of new pharmaceuticals.
TL;DR: This review discusses the origin of this force, its production by different microelectrode designs, and its use for nanomaterials assembly, with a focus on efforts toward heterogeneous integration with on-chip electronics for single-particle characterization and device structures.
Abstract: The force induced on anisotropic nanoparticles in a nonuniform electric field can be used to attract, orient, and position the nanoparticles with respect to microelectrodes on a surface For polarizable nanomaterials, such as nanowires, carbon nanotubes, or graphene sheets suspended in solvent, this dielectrophoretic force results in movement to regions of highest electric field strength This review discusses the origin of this force, its production by different microelectrode designs, and its use for nanomaterials assembly, with a focus on efforts toward heterogeneous integration with on-chip electronics for single-particle characterization and device structures
TL;DR: A guideline for the size-consistent design of electronic and vibrational methods is proposed and the extensive-intensive consistency theorem is introduced, which stipulates the precise balance between the determinant spaces reached by extensive and intensive operators.
Abstract: A pedagogical proof is presented for the extensivity of energies of metallic and nonmetallic crystals that proceeds by elucidating the asymptotic distance dependence of the effective chemical interactions: kinetic, Coulomb, exchange, and correlation. On this basis, a guideline for the size-consistent design of electronic and vibrational methods is proposed. This guideline underscores the significance of the distinct use of the intermediate and standard normalization of wave functions for extensive and intensive quantities, includes the extensive and intensive diagram theorems as the unambiguous criteria for determining size consistency of a method for extensive and intensive quantities, and introduces the extensive-intensive consistency theorem, which stipulates the precise balance between the determinant spaces reached by extensive and intensive operators. Electronic and vibrational methods for crystals are reviewed that are inspired by these formal analyses or developed in accordance with the guideline.
TL;DR: The origin of the novel behavior of CO molecules in the electronic and geometrical properties of the quasi-one-dimensional substrate suggests that similar molecule-molecule and molecule-substrate interactions could play an important role at catalytic sites on reactive surfaces.
Abstract: By low-temperature scanning tunneling microscopy, we study CO molecule chemisorption on a quasi-one-dimensional Cu(110)-(2×1)-O surface. Atom-resolved images reveal how the interaction of CO with the surface Cu-O- chains gives rise to orthogonal attractive and repulsive intermolecular interactions. First-principles calculations show that CO molecules induce unprecedented lifting of the host Cu atoms by 1 A from the Cu-O- chains, enabling the Cu-CO unit to tilt by 45° from the surface normal. Contrary to the behavior of CO on metal surfaces, this structural distortion enables unprecedented, orthogonal, short-range intermolecular dipole-dipole attraction and long-range, surface-mediated repulsion. These interactions lead to self-assembly into molecular nanograting structures consisting of arrays of single-molecule-wide CO rows. The origin of the novel behavior of CO molecules in the electronic and geometrical properties of the quasi-one-dimensional substrate suggests that similar molecule-molecule and molecule-substrate interactions could play an important role at catalytic sites on reactive surfaces.