Single-bond formation and characterization with a scanning tunneling microscope

A scanning tunneling microscope (STM) was used to manipulate the bonding of a carbon monoxide (CO) molecule and to analyze the structure and vibrational properties of individual products. Individual iron (Fe) atoms were evaporated and coadsorbed with CO molecules on a silver (110) surface at 13 kelvin. A CO molecule was transferred from the surface to the STM tip and bonded with an Fe atom to form Fe(CO). A second CO molecule was similarly transferred and bonded with Fe(CO) to form Fe(CO)(2). Controlled bond formation and characterization at the single-bond level probe chemistry at the spatial limit.     

Direct observation and quantification of CO₂ binding within an amine-functionalized nanoporous solid

Understanding the molecular details of CO(2)-sorbent interactions is critical for the design of better carbon-capture systems. Here we report crystallographic resolution of CO(2) molecules and their binding domains in a metal-organic framework functionalized with amine groups. Accompanying computational studies that modeled the gas sorption isotherms, high heat of adsorption, and CO(2) lattice positions showed high agreement on all three fronts. The modeling apportioned specific binding interactions for each CO(2) molecule, including substantial cooperative binding effects among the guest molecules. The validation of the capacity of such simulations to accurately model molecular-scale binding bodes well for the theory-aided development of amine-based CO(2) sorbents. The analysis shows that the combination of appropriate pore size, strongly interacting amine functional groups, and the cooperative binding of CO(2) guest molecules is responsible for the low-pressure binding and large uptake of CO(2) in this sorbent material.     

小分子气体在聚叔丁基乙炔中扩散溶解行为的分子动力学模拟

采用分子动力学和巨正则Monte Carlo(GCMC)法研究了小分子(H2,O2,CO2,N2,CH4)在聚叔丁基乙炔中的扩散和溶解行为,应用自由体积理论探讨了小分子在聚合物内的扩散机理.结果表明,分子越小,其在聚合物内运动范围越大,扩散系数越大.模拟所得的扩散和溶解系数与实验值吻合较好,同时验证了扩散系数与分子有效直径的关系.计算所得渗透系数,与文献报道的实验数据在同一数量级上,说明分子动力学和蒙特卡洛模拟是研究小分子在聚合物中扩散溶解行为的有效方法.     

Selective bond dissociation and rearrangement with optimally tailored, strong-field laser pulses

We used strong-field laser pulses that were tailored with closed-loop optimal control to govern specified chemical dissociation and reactivity channels in a series of organic molecules. Selective cleavage and rearrangement of chemical bonds having dissociation energies up to approximately 100 kilocalories per mole (about 4 electron volts) are reported for polyatomic molecules, including (CH3)2CO (acetone), CH3COCF3 (trifluoroacetone), and C6H5COCH3 (acetophenone). Control over the formation of CH(3)CO from (CH3)2CO, CF3 (or CH3) from CH3COCF3, and C6H5CH3 (toluene) from C6H5COCH3 was observed with high selectivity. Strong-field control appears to have generic applicability for manipulating molecular reactivity because the tailored intense laser fields (about 10(13) watts per square centimeter) can dynamically Stark shift many excited states into resonance, and consequently, the method is not confined by resonant spectral restrictions found in the perturbative (weak-field) regime.     

The hydroperoxyl radical in atmospheric chemical dynamics: reaction with carbon monoxide

From measurements of the photochemical rate of production of CO(2)(16,18) and CO(2)(16,16), produced from the low intensity photolysis of mixtures of CO, H(2)O, Ar, and O(2)(18,18), the rate constant for the reaction HO(2) + CO --> CO(2) + OH has been determined at 300 degrees K to be less than or equal to 10(-20) cubic centimeter per molecule per second. These measurements indicate that the reaction of thermalized HO(2) is of negligible importance as a sink mechanism for converting CO to CO(2) in either the troposphere or the stratosphere.     

Chemical cartography: finding the keys to the kinetic labyrinth

Very high resolution lasers allow spectroscopic pictures to be taken following a collision between two molecular reactants. The features of these "pictures" are the electronic, vibrational, rotational, and translational motions of the atomic particles, which relate the quantum states of the reactants to the quantum states of the products. Such state-to-state kinetic information can be used to test the shape and nature of the interaction potential that controls the collision process. The potential itself is akin to a map of the terrain through mountains and valleys where elevation is a measure of energy instead of height. Accurate mapping of this potential surface leads to an understanding of the forces which control rates and mechanisms of chemical reactions. The application of four different advanced laser techniques to the study of collisions between "hot" hydrogen(H) atoms and carbon dioxide(CO(2)) molecules has provided a wealth of information about both reactive and nonreactive collisions for this system. The availability of data for rotationally, vibrationally, and translationally inelastic excitation of CO(2) by H atoms, when compared with data for reactive events producing OH + CO, provides insights into the dynamics of collisions between H and CO(2), and illustrates the future promise of these powerful techniques for elucidating features of potential energy surfaces.     

Determining transition-state geometries in liquids using 2D-IR

Many properties of chemical reactions are determined by the transition state connecting reactant and product, yet it is difficult to directly obtain any information about these short-lived structures in liquids. We show that two-dimensional infrared (2D-IR) spectroscopy can provide direct information about transition states by tracking the transformation of vibrational modes as a molecule crossed a transition state. We successfully monitored a simple chemical reaction, the fluxional rearrangement of Fe(CO)5, in which the exchange of axial and equatorial CO ligands causes an exchange of vibrational energy between the normal modes of the molecule. This energy transfer provides direct evidence regarding the time scale, transition state, and mechanism of the reaction.     

Theoretical organometallic chemistry

Organometallic chemists have synthesized a remarkable variety of new structural types. In these structures ligands, which are organic or inorganic molecules of variable independent stability, bind to one or more transition metal atoms. An approach to an understanding of the electronic structure, geometrical preferences, and reactivity of these complexes may be made if the molecule is "decomposed" conceptually into a metal fragment, ML(n), and a ligand. A library of the molecular orbitals of these fragments is becoming available. One then "reconstructs" the molecule by examining the interaction of the orbitals of the ligand, typically an organic molecule, with the orbitals of the ML(n), fragment.     

A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea

The assimilation of carbon dioxide (CO2) into organic material is quantitatively the most important biosynthetic process. We discovered that an autotrophic member of the archaeal order Sulfolobales, Metallosphaera sedula, fixed CO2 with acetyl-coenzyme A (acetyl-CoA)/propionyl-CoA carboxylase as the key carboxylating enzyme. In this system, one acetyl-CoA and two bicarbonate molecules were reductively converted via 3-hydroxypropionate to succinyl-CoA. This intermediate was reduced to 4-hydroxybutyrate and converted into two acetyl-CoA molecules via 4-hydroxybutyryl-CoA dehydratase. The key genes of this pathway were found not only in Metallosphaera but also in Sulfolobus, Archaeoglobus, and Cenarchaeum species. Moreover, the Global Ocean Sampling database contains half as many 4-hydroxybutyryl-CoA dehydratase sequences as compared with those found for another key photosynthetic CO2-fixing enzyme, ribulose-1,5-bisphosphate carboxylase-oxygenase. This indicates the importance of this enzyme in global carbon cycling.     

Erratum

The cover caption for the issue of 9 February 1990 should have described the molecule on the cover as VPI-5 (Dow and Virginia Polytechnic Institute), not as ALPO-5 (Union Carbide). The first sentence of the caption should have read, "Superlattices of p-nitroaniline molecules self-assemble and orient within the polar, greater than 10 angstrom wide channels of VIP-5, a molecular sieve." The preferred orientation of the polar molecules occurs in both materials.     

Trends in Stomatal Density and 13C/12C Ratios of Pinus flexilis Needles During Last Glacial-Interglacial Cycle

Measurements of stomatal density and delta(13)C of limber pine (Pinus flexilis) needles (leaves) preserved in pack rat middens from the Great Basin reveal shifts in plant physiology and leaf morphology during the last 30,000 years. Sites were selected so as to offset glacial to Holocene climatic differences and thus to isolate the effects of changing atmospheric CO(2) levels. Stomatal density decreased approximately 17 percent and delta(13)C decreased approximately 1.5 per mil during deglaciation from 15,000 to 12,000 years ago, concomitant with a 30 percent increase in atmospheric CO(2). Water-use efficiency increased approximately 15 percent during deglaciation, if temperature and humidity were held constant and the proxy values for CO(2) and delta(13)C of past atmospheres are accurate. The delta(13)C variations may help constrain hypotheses about the redistribution of carbon between the atmosphere and biosphere during the last glacial-interglacial cycle.     

Generalized tube model of biased reptation for gel electrophoresis of DNA

A theoretical analysis of the reptational motion of DNA in a gel that includes the effects of molecular fluctuations has been used to explain the main features found in experiments involving periodic inversion of the electric field. The resonance-like decrease of the electrophoretic mobility as a function of pulse duration is related to transient "undershoots" in the orientation of the molecule, in agreement with recent experimental data. These features arise from a delicate interplay of internal and center of mass motion of the molecules under pulsed field conditions, and are important for the separation of DNA molecules in the size range 0.2 to 10 million base pairs.     

Food for thought: lower-than-expected crop yield stimulation with rising CO2 concentrations

Model projections suggest that although increased temperature and decreased soil moisture will act to reduce global crop yields by 2050, the direct fertilization effect of rising carbon dioxide concentration ([CO2]) will offset these losses. The CO2 fertilization factors used in models to project future yields were derived from enclosure studies conducted approximately 20 years ago. Free-air concentration enrichment (FACE) technology has now facilitated large-scale trials of the major grain crops at elevated [CO2] under fully open-air field conditions. In those trials, elevated [CO2] enhanced yield by approximately 50% less than in enclosure studies. This casts serious doubt on projections that rising [CO2] will fully offset losses due to climate change.     

C_2H_4分子红外吸收特性的光声探测

用ＴＥＡＣＯ２激光做激发源，用光声法检测了９．２～１０．８μｍ波长范围内Ｃ２Ｈ４分子的红外吸收特性，获得了Ｃ２Ｈ４分子的单脉冲激光光声谱，它与Ｃ２Ｈ４分子的红外吸收谱及光热谱符合的较好；并用光声法测得了样品气体中的声速及Ｃ２Ｈ４分子的Ｖ－Ｔ驰豫时间。     

Kuwait oil fires: correction

In our article "Airborne studies of the smoke from the Kuwait oil fires" (15 May, p. 987) (1), we stated that the depletions of sulfur dioxide (SO(2)) and nitrogen oxides (NO(x)) in the smoke plume from the Kuwait oil fires were 50 and 60% per hour, respectively. These values were derived from measurements made aboard a Convair C-131 aircraft, and measurements of CO(2) were used as a conserved tracer. Subsequent comparisons of these measurements of CO(2) (which were obtained from a continuous analyzer) with independent measurements of CO(2) (obtained from "grab" samples) revealed that the continuous CO(2) measurements were occasionally contaminated by cabin air. Recalculation of the depletion rates of SO(2) and NO(x), with the use of uncontaminated measurements of CO(2) from the "grab" sampler aboard the aircraft yielded values of 6 and 22%, respectively (2). Our conclusions with regard to the climatic effects of the Kuwait oil fires are unchanged.     

Molecule cascades

Carbon monoxide molecules were arranged in atomically precise configurations, which we call "molecule cascades," where the motion of one molecule causes the subsequent motion of another, and so on in a cascade of motion similar to a row of toppling dominoes. Isotopically pure cascades were assembled on a copper (111) surface with a low-temperature scanning tunneling microscope. The hopping rate of carbon monoxide molecules in cascades was found to be independent of temperature below 6 kelvin and to exhibit a pronounced isotope effect, hallmarks of a quantum tunneling process. At higher temperatures, we observed a thermally activated hopping rate with an anomalously low Arrhenius prefactor that we interpret as tunneling from excited vibrational states. We present a cascade-based computation scheme that has all of the devices and interconnects required for the one-time computation of an arbitrary logic function. Logic gates and other devices were implemented by engineered arrangements of molecules at the intersections of cascades. We demonstrate a three-input sorter that uses several AND gates and OR gates, as well as the crossover and fan-out units needed to connect them.     

Free energy and temperature dependence of electron transfer at the metal-electrolyte interface

The rate constant of the electron-transfer reaction between a gold electrode and an electroactive ferrocene group has been measured at a structurally well-defined metal-electrolyte interface at temperatures from 1 degrees to 47 degrees C and reaction free energies from -1.0 to +0.8 electron volts (eV). The ferrocene group was positioned a fixed distance from the gold surface by the self-assembly of a mixed thiol monolayer of (eta(5)C(5)H(5))Fe(eta(5)C(5)H(4))CO(2)(CH(2))(16)SH and CH(3)(CH(2))(15)SH. Rate constants from 1 per second (s(-1)) to 2 x 10(4) s(-1) in 1 molar HClO(4) are reasonably fit with a reorganization energy of 0.85 eV and a prefactor for electron tunneling of 7 x 10(4) s(-1) eV(-1). Such self-assembled monolayers can be used to systematically probe the dependence of electron-transfer rates on distance, medium, and spacer structure, and to provide an empirical basis for the construction of interfacial devices such as sensors and transducers that utilize macroscopically directional electron-transfer reactions.     

Molecular conformation of dihydrouridine: puckered base nucleoside of transfer RNA

The crystal structure of dihydrouridine hemihydrate has been determined by x-ray diffraction. Crystals of dihydrouridine contain two independent molecules in the asymmetric unit and a molecule of water. The x-ray structure determination has shown that the conformations of both molecules differ in important respects in the saturated base and the ribose. The molecular conformation of dihydrouridine has, for the first time, provided structural evidence that the rare nucleoside can proinote "loop" formation in the sugar-phosphate chain.     

Detection of near-atmospheric concentrations of CO2 by an olfactory subsystem in the mouse

Carbon dioxide (CO2) is an important environmental cue for many organisms but is odorless to humans. It remains unclear whether the mammalian olfactory system can detect CO2 at concentrations around the average atmospheric level (0.038%). We demonstrated the expression of carbonic anhydrase type II (CAII), an enzyme that catabolizes CO2, in a subset of mouse olfactory neurons that express guanylyl cyclase D (GC-D+ neurons) and project axons to necklace glomeruli in the olfactory bulb. Exposure to CO2 activated these GC-D+ neurons, and exposure of a mouse to CO2 activated bulbar neurons associated with necklace glomeruli. Behavioral tests revealed CO2 detection thresholds of approximately 0.066%, and this sensitive CO2 detection required CAII activity. We conclude that mice detect CO2 at near-atmospheric concentrations through the olfactory subsystem of GC-D+ neurons.     

The process of tholin formation in Titan's upper atmosphere

Titan's lower atmosphere has long been known to harbor organic aerosols (tholins) presumed to have been formed from simple molecules, such as methane and nitrogen (CH4 and N2). Up to now, it has been assumed that tholins were formed at altitudes of several hundred kilometers by processes as yet unobserved. Using measurements from a combination of mass/charge and energy/charge spectrometers on the Cassini spacecraft, we have obtained evidence for tholin formation at high altitudes (approximately 1000 kilometers) in Titan's atmosphere. The observed chemical mix strongly implies a series of chemical reactions and physical processes that lead from simple molecules (CH4 and N2) to larger, more complex molecules (80 to 350 daltons) to negatively charged massive molecules (approximately 8000 daltons), which we identify as tholins. That the process involves massive negatively charged molecules and aerosols is completely unexpected.