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- Volume 59, 2008
Annual Review of Physical Chemistry - Volume 59, 2008
Volume 59, 2008
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Functional Polymer Brushes in Aqueous Media from Self-Assembled and Surface-Initiated Polymers
Vol. 59 (2008), pp. 493–517More LessThis review focuses on the behavior of single-component, water-soluble neutral and charged brushes. Selected examples illustrate how solvation effects, hydrophobic interactions, and electrostatic interactions create complex behaviors not easily captured in mean-field treatments. In particular, we distinguish between two classes of polymer brushes: those that can be described classically within the context of generalized van der Waals potentials and those that can be described by model-dependent potentials arising from specific interactions. In classical systems, only a few global parameters are needed to predict behavior. Nonclassical systems, in contrast, necessitate several local details, which do not necessarily lead to universal scaling laws. Although these nonclassical interactions present unique opportunities for engineering functional surfaces, they also present new challenges for designing well-defined systems with precise control over distributions in the degree of polymerization and tethering density.
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Electronic Spectroscopy of Carbon Chains
Vol. 59 (2008), pp. 519–544More LessInvestigators have recorded the electronic spectra of assorted carbon-chain systems in the gas phase using a variety of methods, ranging from direct cavity ringdown absorption spectroscopy to photofragmentation techniques that utilize the cooling capabilities of an ion trap. We summarize the results from these studies and compare them with astronomical measurements of the diffuse interstellar band (DIB) absorptions. Although carbon chains comprising up to a handful of carbon atoms cannot be the carrier species, we explore which chains remain viable. In particular, the 1Σu+–X1Σg+ transitions of the odd-numbered carbon chains (n = 17,19,…) possess large oscillator strengths and lie in the 400–900-nm DIB range. The origin bands of larger bare carbon rings, such as C18, have also been observed, with striking similarities to some DIB measurements at high resolution, although at other wavelengths. Finally, we consider recently obtained electronic spectra of metal-containing carbon chains.
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Multiscale Simulation of Soft Matter: From Scale Bridging to Adaptive Resolution
Vol. 59 (2008), pp. 545–571More LessThe relation between atomistic chemical structure, molecular architecture, molecular weight, and material properties is of basic concern in modern soft material science and includes standard properties of bulk materials and surface and interface aspects, as well as the relation between structure and function in nanoscopic objects and molecular assemblies of both synthetic and biological origin. This all implies a thorough understanding on many length and correspondingly time scales, ranging from (sub)atomistic to macroscopic. Presently, computer simulations play an increasingly important, if not central, role. Some problems do not require specific atomistic details, whereas others require them only locally. However, in many cases this strict separation is not sufficient for a comprehensive understanding of systems, and flexible simulation schemes are required that link the different levels of resolution. We here give a general view of the problem regarding soft matter and discuss some specific examples of linked simulation techniques at different resolution levels. We then discuss a recently developed flexible simulation scheme, the AdResS method, which allows one to adaptively change the resolution in certain regions of space on demand.
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Free Energies of Chemical Reactions in Solution and in Enzymes with Ab Initio Quantum Mechanics/Molecular Mechanics Methods
Hao Hu, and Weitao YangVol. 59 (2008), pp. 573–601More LessCombined quantum mechanics/molecular mechanics (QM/MM) methods provide an accurate and efficient energetic description of complex chemical and biological systems, leading to significant advances in the understanding of chemical reactions in solution and in enzymes. Here we review progress in QM/MM methodology and applications, focusing on ab initio QM-based approaches. Ab initio QM/MM methods capitalize on the accuracy and reliability of the associated quantum-mechanical approaches, however, at a much higher computational cost compared with semiempirical quantum-mechanical approaches. Thus reaction-path and activation free-energy calculations based on ab initio QM/MM methods encounter unique challenges in simulation timescales and phase-space sampling. This review features recent developments overcoming these challenges and enabling accurate free-energy determination for reaction processes in solution and in enzymes, along with applications.
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Fluctuation Theorems
Vol. 59 (2008), pp. 603–633More LessFluctuation theorems, developed over the past 15 years, have resulted in fundamental breakthroughs in our understanding of how irreversibility emerges from reversible dynamics and have provided new statistical mechanical relationships for free-energy changes. They describe the statistical fluctuations in time-averaged properties of many-particle systems such as fluids driven to nonequilibrium states and provide some of the few analytical expressions that describe nonequilibrium states. Quantitative predictions on fluctuations in small systems that are monitored over short periods can also be made, and therefore the fluctuation theorems allow thermodynamic concepts to be extended to apply to finite systems. For this reason, we anticipate an important role for fluctuation theorems in the design of nanotechnological devices and in the understanding of biological processes. This review discusses these theorems, their physical significance, and results for experimental and model systems.
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Structure, Dynamics, and Assembly of Filamentous Bacteriophages by Nuclear Magnetic Resonance Spectroscopy
Vol. 59 (2008), pp. 635–657More LessFilamentous bacteriophages serve as model systems for the development and implementation of spectroscopic methods suitable for biological supramolecular assemblies. Not only are their coat proteins small and readily prepared in the laboratory, but they also have two primary roles as membrane proteins and as the principal structural element of the virus particles. As a bacterial system, they are readily labeled with stable isotopes, and this has opened possibilities for the many nuclear magnetic resonance (NMR) studies described in this review. In particular, solid-state NMR of aligned samples has been used to determine the three-dimensional structures of both the membrane-bound forms of coat proteins in phospholipid bilayers and structural forms in virus particles, which has led to an analysis of the assembly mechanism for virus particles as they are extruded through the cell membrane.
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Inside a Collapsing Bubble: Sonoluminescence and the Conditions During Cavitation
Vol. 59 (2008), pp. 659–683More LessAcoustic cavitation, the growth and rapid collapse of bubbles in a liquid irradiated with ultrasound, is a unique source of energy for driving chemical reactions with sound, a process known as sonochemistry. Another consequence of acoustic cavitation is the emission of light [sonoluminescence (SL)]. Spectroscopic analyses of SL from single bubbles as well as a cloud of bubbles have revealed line and band emission, as well as an underlying continuum arising from a plasma. Application of spectrometric methods of pyrometry as well as tools of plasma diagnostics to relative line intensities, profiles, and peak positions have allowed the determination of intracavity temperatures and pressures. These studies have shown that extraordinary conditions (temperatures up to 20,000 K; pressures of several thousand bar; and heating and cooling rates of >1012 K s−1) are generated within an otherwise cold liquid.
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Elastic Modeling of Biomembranes and Lipid Bilayers
Vol. 59 (2008), pp. 685–712More LessThe simulation of biological membranes over length and time scales relevant to cellular biology is not currently feasible using conventional (fully atomic or molecularly detailed) simulation strategies. Given the wide disparity between what is possible on today's computers and the problems one might like to study, it seems unlikely this situation will change for several decades. An appealing alternative to traditional computational approaches is to employ simpler, continuum-based models developed within the frameworks of elasticity theory, fluid dynamics, and statistical mechanics. Although such models have seen wide use in analytical descriptions of membrane behavior, the extension of these methods to more general situations and numerical analysis is just beginning to be explored. This article reviews continuum models for membrane behavior with an emphasis on the use of such models in computational studies. Two applications are explored to demonstrate the utility of this level of coarse-grained modeling.
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Water in Nonpolar Confinement: From Nanotubes to Proteins and Beyond*
Vol. 59 (2008), pp. 713–740More LessWater molecules confined to nonpolar pores and cavities of nanoscopic dimensions exhibit highly unusual properties. Water filling is strongly cooperative, with the possible coexistence of filled and empty states and sensitivity to small perturbations of the pore polarity and solvent conditions. Confined water molecules form tightly hydrogen-bonded wires or clusters. The weak attractions to the confining wall, combined with strong interactions between water molecules, permit exceptionally rapid water flow, exceeding expectations from macroscopic hydrodynamics by several orders of magnitude. The proton mobility along 1D water wires also substantially exceeds that in the bulk. Proteins appear to exploit these unusual properties of confined water in their biological function (e.g., to ensure rapid water flow in aquaporins or to gate proton flow in proton pumps and enzymes). The unusual properties of water in nonpolar confinement are also relevant to the design of novel nanofluidic and molecular separation devices or fuel cells.
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High-Resolution Spectroscopic Studies and Theory of Parity Violation in Chiral Molecules
Vol. 59 (2008), pp. 741–769More LessWe review the high-resolution spectroscopic approach toward the study of intramolecular dynamics, emphasizing molecular parity violation. Theoretical work in the past decade has shown that parity-violating potentials in chiral molecules are much larger (typically one to two orders of magnitude) than anticipated on the basis of older theories. This makes experimental approaches toward small molecular parity-violating effects promising. The concepts and results of intramolecular dynamics derived from spectroscopy are analyzed as a sequence of symmetry breakings. We summarize the concepts of symmetry breakings (de facto and de lege) in view of parity violation in chiral molecules. The experimental schemes and the current status of spectroscopic experiments on molecular parity violation are established. We discuss the promises of detecting and accurately measuring parity-violating energy differences ΔpvE on the order of 10−11 J mol−1 (approximately 100 aeV) in enantiomers of chiral molecules with regard to their contribution to fundamental physics in the framework of the standard model of particle physics and more speculative future fundamental symmetry tests such as for the combined charge conjugation, parity, and time-reversal (CPT) symmetry violation.
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Collapse Mechanisms of Langmuir Monolayers
Vol. 59 (2008), pp. 771–791More LessWhen a two-dimensional (2D) film is compressed to its stability limit, it explores the third dimension via collapse. Understanding this 2D-to-3D transition is of great importance as it provides insight into the origin of defects in thin films. This review draws attention to a reversible folding collapse first discovered in model lung surfactant systems and explores the driving forces for this mechanism. The mode of collapse can be tuned by varying the mechanical properties of the film. I present a continuum elastic theory that captures the onset of the observed folding instability and use digital image analysis to analyze the folding dynamics. This article further explores factors that determine the maximum surface pressure a mixed monolayer can sustain and explains the observed phenomenon using the principle of rigidity percolation. The folding transition observed in lipid monolayers described here has also been observed in other systems, including monolayers of nanoparticles.
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Previous Volumes
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Volume 75 (2024)
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Volume 74 (2023)
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Volume 73 (2022)
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Volume 72 (2021)
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Volume 71 (2020)
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Volume 70 (2019)
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Volume 69 (2018)
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Volume 68 (2017)
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Volume 67 (2016)
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Volume 66 (2015)
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Volume 65 (2014)
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Volume 64 (2013)
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Volume 63 (2012)
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Volume 62 (2011)
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Volume 61 (2010)
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Volume 60 (2009)
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Volume 59 (2008)
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Volume 58 (2007)
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Volume 57 (2006)
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Volume 56 (2005)
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Volume 55 (2004)
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Volume 54 (2003)
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Volume 53 (2002)
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Volume 52 (2001)
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Volume 51 (2000)
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Volume 50 (1999)
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Volume 49 (1998)
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Volume 48 (1997)
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Volume 47 (1996)
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Volume 46 (1995)
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Volume 45 (1994)
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Volume 44 (1993)
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Volume 43 (1992)
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Volume 42 (1991)
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Volume 41 (1990)
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Volume 40 (1989)
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Volume 39 (1988)
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Volume 38 (1987)
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Volume 37 (1986)
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Volume 36 (1985)
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Volume 35 (1984)
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Volume 34 (1983)
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Volume 33 (1982)
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Volume 32 (1981)
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Volume 31 (1980)
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Volume 30 (1979)
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Volume 29 (1978)
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Volume 28 (1977)
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Volume 27 (1976)
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Volume 26 (1975)
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Volume 25 (1974)
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Volume 24 (1973)
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Volume 23 (1972)
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Volume 22 (1971)
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Volume 21 (1970)
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Volume 20 (1969)
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Volume 19 (1968)
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Volume 18 (1967)
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Volume 17 (1966)
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Volume 16 (1965)
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Volume 15 (1964)
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Volume 14 (1963)
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Volume 13 (1962)
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Volume 12 (1961)
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Volume 11 (1960)
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Volume 10 (1959)
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Volume 9 (1958)
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Volume 8 (1957)
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Volume 7 (1956)
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Volume 6 (1955)
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Volume 5 (1954)
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Volume 4 (1953)
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Volume 3 (1952)
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Volume 2 (1951)
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Volume 1 (1950)
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Volume 0 (1932)