Showing papers on "Molecule published in 2007"
TL;DR: In this paper, the authors carried out a natural bond order B3LYP analysis of the molecules CF(3)X, with X = F, Cl, Br and I. The results showed that the Cl and Br atoms in these molecules closely approximate the [Formula: see text] configuration, where the z-axis is along the R-X bond.
Abstract: Halogen bonding refers to the non-covalent interactions of halogen atoms X in some molecules, RX, with negative sites on others. It can be explained by the presence of a region of positive electrostatic potential, the sigma-hole, on the outermost portion of the halogen's surface, centered on the R-X axis. We have carried out a natural bond order B3LYP analysis of the molecules CF(3)X, with X = F, Cl, Br and I. It shows that the Cl, Br and I atoms in these molecules closely approximate the [Formula: see text] configuration, where the z-axis is along the R-X bond. The three unshared pairs of electrons produce a belt of negative electrostatic potential around the central part of X, leaving the outermost region positive, the sigma-hole. This is not found in the case of fluorine, for which the combination of its high electronegativity plus significant sp-hybridization causes an influx of electronic charge that neutralizes the sigma-hole. These factors become progressively less important in proceeding to Cl, Br and I, and their effects are also counteracted by the presence of electron-withdrawing substituents in the remainder of the molecule. Thus a sigma-hole is observed for the Cl in CF(3)Cl, but not in CH(3)Cl.
1,893 citations
TL;DR: An iron (Fe)–based small molecule catalyst that uses hydrogen peroxide (H2O2) to oxidize a broad range of substrates and Predictable selectivity is achieved solely on the basis of the electronic and steric properties of the C–H bonds, without the need for directing groups.
Abstract: Realizing the extraordinary potential of unactivated sp3 C–H bond oxidation in organic synthesis requires the discovery of catalysts that are both highly reactive and predictably selective. We report an iron (Fe)–based small molecule catalyst that uses hydrogen peroxide (H2O2) to oxidize a broad range of substrates. Predictable selectivity is achieved solely on the basis of the electronic and steric properties of the C–H bonds, without the need for directing groups. Additionally, carboxylate directing groups may be used to furnish five-membered ring lactone products. We demonstrate that these three modes of selectivity enable the predictable oxidation of complex natural products and their derivatives at specific C–H bonds with preparatively useful yields. This type of general and predictable reactivity stands to enable aliphatic C–H oxidation as a method for streamlining complex molecule synthesis.
1,030 citations
TL;DR: Methods to overcome the inability of almost all current density functionals to describe the ubiquitous attractive long-range van der Waals (dispersion) interactions are reviewed, and a very successful correction is described that is based on damped -C(6).R(-6) potentials (DFT-D).
Abstract: Kohn–Sham density functional theory (KS-DFT) is nowadays the most widely used quantum chemical method for electronic structure calculations in chemistry and physics. Its further application in e.g. supramolecular chemistry or biochemistry has mainly been hampered by the inability of almost all current density functionals to describe the ubiquitous attractive long-range van der Waals (dispersion) interactions. We review here methods to overcome this defect, and describe in detail a very successful correction that is based on damped –C6·R–6 potentials (DFT-D). As examples we consider the non-covalent inter- and intra-molecular interactions in unsaturated organic molecules (so-called π–π stacking in benzenes and dyes), in biologically relevant systems (nucleic acid bases/pairs, proteins, and ‘folding’ models), between fluorinated molecules, between curved aromatics (corannulene and carbon nanotubes) and small molecules, and for the encapsulation of methane in water clusters. In selected cases we partition the interaction energies into the most relevant contributions from exchange-repulsion, electrostatics, and dispersion in order to provide qualitative insight into the binding character.
663 citations
TL;DR: Evidence is presented for hydrogen multicentre bonds -a generalization of three-centre bonds-in which a hydrogen atom equally bonds to four or more other atoms, when substituting for oxygen in metal oxides, which are remarkably strong despite their large hydrogen-metal distances.
Abstract: The concept of a chemical bond stands out as a major development in the process of understanding how atoms are held together in molecules and solids. Lewis’ classical picture of chemical bonds as shared-electron pairs1 evolved to the quantum-mechanical valence-bond and molecular-orbital theories2,3, and the classification of molecules and solids in terms of their bonding type: covalent, ionic, van der Waals and metallic. Along with the more complex hydrogen bonds4 and three-centre bonds5,6, they form a paradigm within which the structure of almost all molecules and solids can be understood. Here, we present evidence for hydrogen multicentre bonds—a generalization of three-centre bonds—in which a hydrogen atom equally bonds to four or more other atoms. When substituting for oxygen in metal oxides, hydrogen bonds equally to all the surrounding metal atoms, becoming fourfold coordinated in ZnO, and sixfold coordinated in MgO. These multicentre bonds are remarkably strong despite their large hydrogen–metal distances. The calculated local vibration mode frequency in MgO agrees with infrared spectroscopy measurements7. Multicoordinated hydrogen also explains the dependence of electrical conductivity on oxygen partial pressure, resolving a long-standing controversy on the role of point defects in unintentional n-type conductivity of ZnO (refs 8–10).
630 citations
TL;DR: A coupling of the switching process so that the charge injection in one molecule induced tautomerization in an adjacent molecule is demonstrated.
Abstract: The bistability in the position of the two hydrogen atoms in the inner cavity of single free-base naphthalocyanine molecules constitutes a two-level system that was manipulated and probed by low-temperature scanning tunneling microscopy. When adsorbed on an ultrathin insulating film, the molecules can be switched in a controlled fashion between the two states by excitation induced by the inelastic tunneling current. The tautomerization reaction can be probed by resonant tunneling through the molecule and is expressed as considerable changes in the conductivity of the molecule. We also demonstrated a coupling of the switching process so that the charge injection in one molecule induced tautomerization in an adjacent molecule.
627 citations
TL;DR: A simple method to place target molecules specifically at two diametrically opposed positions in the molecular coating of metal nanoparticles, based on the functionalization of the polar singularities that must form when a curved surface is coated with ordered monolayers, such as a phase-separated mixture of ligands.
Abstract: Nanoparticles can be used as the building blocks for materials such as supracrystals or ionic liquids. However, they lack the ability to bond along specific directions as atoms and molecules do. We report a simple method to place target molecules specifically at two diametrically opposed positions in the molecular coating of metal nanoparticles. The approach is based on the functionalization of the polar singularities that must form when a curved surface is coated with ordered monolayers, such as a phase-separated mixture of ligands. The molecules placed at these polar defects have been used as chemical handles to form nanoparticle chains that in turn can generate self-standing films.
614 citations
TL;DR: It is found that water molecules in the hydration shell of K+ are orientationally more disordered than those hydrating a Na+ ion and are inclined to orient their dipole moments tangentially to the Hydration sphere.
Abstract: Neutron diffraction data with hydrogen isotope substitution on aqueous solutions of NaCl and KCl at concentrations ranging from high dilution to near-saturation are analyzed using the Empirical Potential Structure Refinement technique. Information on both the ion hydration shells and the microscopic structure of the solvent is extracted. Apart from obvious effects due to the different radii of the three ions investigated, it is found that water molecules in the hydration shell of K+ are orientationally more disordered than those hydrating a Na+ ion and are inclined to orient their dipole moments tangentially to the hydration sphere. Cl- ions form instead hydrogen-bonded bridges with water molecules and are readily accommodated into the H-bond network of water. The results are used to show that concepts such as structure maker/breaker, largely based on thermodynamic data, are not helpful in understanding how these ions interact with water at the molecular level.
587 citations
TL;DR: Two different techniques indicate that the interaction of water with anions is by an approximately linear hydrogen bond, suggesting that the dominant forces on ions in water are short range forces of a chemical nature.
571 citations
TL;DR: In this article, a molecular origin of the striking rate increase observed in a reaction on water is studied theoretically, and a method is given for comparing the rate constants of different rate processes, homogeneous, neat and on-water, all of which have different units, by introducing models that reduce them to the same units.
Abstract: A molecular origin of the striking rate increase observed in a reaction on water is studied theoretically. A key aspect of the on-water rate phenomenon is the chemistry between water and reactants that occurs at an oil-water phase boundary. In particular, the structure of water at the oil-water interface of an oil emulsion, in which approximately one in every four interfacial water molecules has a free ("dangling") OH group that protrudes into the organic phase, plays a key role in catalyzing reactions via the formation of hydrogen bonds. Catalysis is expected when these OH's form stronger hydrogen bonds with the transition state than with the reactants. In experiments more than a 5 orders of magnitude enhancement in rate constant was found in a chosen reaction. The structural arrangement at the "oil-water" interface is in contrast to the structure of water molecules around a small hydrophobic solute in homogeneous solution, where the water molecules are tangentially oriented. The latter implies that a breaking of an existing hydrogen-bond network in homogeneous solution is needed in order to permit a catalytic effect of hydrogen bonds, but not for the on-water reaction. Thereby, the reaction in homogeneous aqueous solution is intrinsically slower than the surface reaction, as observed experimentally. The proposed mechanism of rate acceleration is discussed in light of other on-water reactions that showed smaller accelerations in rates. To interpret the results in different media, a method is given for comparing the rate constants of different rate processes, homogeneous, neat and on-water, all of which have different units, by introducing models that reduce them to the same units. The observed deuterium kinetic isotope effect is discussed briefly, and some experiments are suggested that can test the present interpretation and increase our understanding of the on-water catalysis.
538 citations
TL;DR: In this article, the very large breathing effect of a metal-organic framework during CO 2 adsorption is discussed, and an experiment was conducted for the case of CO 2 adaption at room temperature for porous chromium (III) terephthalate MIL-53.
Abstract: The very large breathing effect of a metal-organic framework during CO 2 adsorption is discussed. An experiment was conducted for the case of CO2 adsorption at room temperature for porous chromium (III) terephthalate MIL-53. The structural topology of MIL-53 consists of a 4 4 net with tilted chains of CrIIIO4(OH) 2 octahedra sharing trans hydroxyl groups solid. These chains are linked through the carboxylate groups of the terephthalate ions forming a 3D framework. An in situ solid-state NMR study of the hydration of MIL-53HT showed that the shrinkage that occurred upon insertion of water molecules resulted from the onset of two types of strong hydrogen bonds. The first type involves the hydrogen atoms of water molecules and the oxygen atoms of the bridging carboxylate groups. The second type, which seems to be more energetically favorable, links OH groups to inserted water molecules.
489 citations
TL;DR: Single-molecule chemical reactions with individual single-walled carbon nanotubes were observed through near-infrared photoluminescence microscopy, providing highly efficient sensing of local chemical and physical perturbations.
Abstract: Single-molecule chemical reactions with individual single-walled carbon nanotubes were observed through near-infrared photoluminescence microscopy. The emission intensity within distinct submicrometer segments of single nanotubes changed in discrete steps after exposure to acid, base, or diazonium reactants. The steps were uncorrelated in space and time and reflected the quenching of mobile excitons at localized sites of reversible or irreversible chemical attack. Analysis of step amplitudes revealed an exciton diffusional range of about 90 nanometers, independent of nanotube structure. Each exciton visited about 10,000 atomic sites during its lifetime, providing highly efficient sensing of local chemical and physical perturbations.
TL;DR: The underlying theme of this Critical Review is the relationship between molecular structure and liquid crystalline behaviour in a class of materials referred to as liquid crystal oligomers, and how this molecular architecture has been exploited to address issues in a range of quite different areas and has given rise to potential applications for these materials.
Abstract: The underlying theme of this Critical Review is the relationship between molecular structure and liquid crystalline behaviour in a class of materials referred to as liquid crystal oligomers. For the purposes of this review, a liquid crystal oligomer will be defined as consisting of molecules composed of semi-rigid mesogenic units connected via flexible spacers. Much of the review will be devoted to structure–property relationships in the simplest oligomers, namely dimers, in which just two mesogenic units are connected by a single spacer. Along the way we will see how this molecular architecture has been exploited to address issues in a range of quite different areas and has given rise to potential applications for these materials. On the whole, only compounds in which the mesogenic units are linked essentially in a linear fashion will be considered while structures such as liquid crystal dendrimers and tetrapodes fall outside the scope of this review. The review will be of interest not only to scientists working directly in this area but in particular to those interested in understanding the relationships between structure and properties in polymers, and those designing materials for new applications (231 references).
TL;DR: In this paper, the σ-hole concept and the outer regions of positive electrostatic potential on the outer surfaces of divalently-bonded Group VI atoms were used to explain the noncovalent but highly directional interactions with nucleophiles.
Abstract: It has been observed both experimentally and computationally that some divalently-bonded Group VI atoms interact in a noncovalent but highly directional manner with nucleophiles We show that this can readily be explained in terms of regions of positive electrostatic potential on the outer surfaces of such atoms, these regions being located along the extensions of their existing covalent bonds These positive regions can interact attractively with the lone pairs of nucleophiles The existence of such a positive region is attributed to the presence of a “σ-hole” This term designates the electron-deficient outer lobe of a half-filled p bonding orbital on the Group VI atom The positive regions become stronger as the electronegativity of the atom decreases and its polarizability increases, and as the groups to which it is covalently bonded become more electron-withdrawing We demonstrate computationally that the σ-hole concept and the outer regions of positive electrostatic potential account for the existence, directionalities and strengths of the observed noncovalent interactions
TL;DR: The authors investigate the chemical reactivity of these zigzag edge sites by examining their reaction energetics with common radicals from first principles, and the validity of this concept is verified by comparing the dissociation energies of edge-radical bonds with similar bonds in molecules.
Abstract: The zigzag edge of a graphene nanoribbon possesses a unique electronic state that is near the Fermi level and localized at the edge carbon atoms. The authors investigate the chemical reactivity of these zigzag edge sites by examining their reaction energetics with common radicals from first principles. A "partial radical" concept for the edge carbon atoms is introduced to characterize their chemical reactivity, and the validity of this concept is verified by comparing the dissociation energies of edge-radical bonds with similar bonds in molecules. In addition, the uniqueness of the zigzag-edged graphene nanoribbon is further demonstrated by comparing it with other forms of sp2 carbons, including a graphene sheet, nanotubes, and an armchair-edged graphene nanoribbon.
TL;DR: It is shown that changes in O-H vibrational spectra induced by the alkali halides in liquid water result instead from the actions of ions' electric fields on adjacent water molecules.
Abstract: It is widely believed that the addition of salts to water engenders structural changes in the hydrogen-bond network well beyond the adjacent shell of solvating molecules. Classification of many ions as "structure makers" and "structure breakers" has been based in part on corresponding changes in the vibrational spectra (Raman and IR). Here we show that changes in O-H vibrational spectra induced by the alkali halides in liquid water result instead from the actions of ions' electric fields on adjacent water molecules. Computer simulations that accurately reproduce our experimental measurements suggest that the statistics of hydrogen-bond strengths are only weakly modified beyond this first solvation shell.
TL;DR: The occurrence in nature of proteins with hemagglutinating activity that in later years were shown to be sugar-specific and eventually named lectins has been known since the turn of the 19th century, but until about two decades ago they aroused little interest.
TL;DR: Solid-state nanopore channels that are selective towards single-stranded DNA (ssDNA) are reported, providing a tool to gain fundamental insight into the channel-molecule interactions and the conceptual framework of diffusive molecular transport with particle-channel interactions.
Abstract: Solid-state nanopores have emerged as possible candidates for next-generation DNA sequencing devices. In such a device, the DNA sequence would be determined by measuring how the forces on the DNA molecules, and also the ion currents through the nanopore, change as the molecules pass through the nanopore. Unlike their biological counterparts, solid-state nanopores have the advantage that they can withstand a wide range of analyte solutions and environments. Here we report solid-state nanopore channels that are selective towards single-stranded DNA (ssDNA). Nanopores functionalized with a 'probe' of hair-pin loop DNA can, under an applied electrical field, selectively transport short lengths of 'target' ssDNA that are complementary to the probe. Even a single base mismatch between the probe and the target results in longer translocation pulses and a significantly reduced number of translocation events. Our single-molecule measurements allow us to measure separately the molecular flux and the pulse duration, providing a tool to gain fundamental insight into the channel-molecule interactions. The results can be explained in the conceptual framework of diffusive molecular transport with particle-channel interactions.
TL;DR: Surprisingly, the two strongest adsorption sites that the authors identified are both directly associated with the organic linkers, instead of the ZnN4 clusters, in strong contrast to classical MOFs, where the metal-oxide clusters are the primary adsorptive sites.
Abstract: Using the difference Fourier analysis of neutron powder diffraction data along with first-principles calculations, we reveal detailed structural information such as methyl group orientation, hydrogen adsorption sites, and binding energies within the nanopore structure of ZIF8 (Zn(MeIM)2). Surprisingly, the two strongest adsorption sites that we identified are both directly associated with the organic linkers, instead of the ZnN4 clusters, in strong contrast to classical MOFs, where the metal-oxide clusters are the primary adsorption sites. These observations are important and hold the key to optimizing this new class of ZIF materials for practical hydrogen storage applications. Finally, at high concentration H2-loadings, ZIF8 structure is capable of holding up to 28 H2 molecules (i.e., 4.2 wt %) in the form of highly symmetric novel three-dimensional interlinked H2-nanoclusters with relatively short H2−H2 distances compared to solid H2. Hence, ZIF compounds with robust chemical stability can be also an id...
TL;DR: The observations indicate that the junction zone involves dimerization of polymer chains through Ca2+ coordination according to the egg-box model, which involves polymer chains packed on a hexagonal lattice with a lattice constant a = 0.66 nm.
TL;DR: In this paper, a partial radical concept for the edge carbon atoms is introduced to characterize their chemical reactivity, and the validity of this concept is verified by comparing the dissociation energies of edge-radical bonds with similar bonds in molecules.
Abstract: The zigzag edge of a graphene nanoribbon possesses a unique electronic state that is near the Fermi level and localized at the edge carbon atoms. We investigate the chemical reactivity of these zigzag edge sites by examining their reaction energetics with common radicals from first principles. A "partial radical" concept for the edge carbon atoms is introduced to characterize their chemical reactivity, and the validity of this concept is verified by comparing the dissociation energies of edge-radical bonds with similar bonds in molecules. In addition, the uniqueness of the zigzag-edged graphene nanoribbon is further demonstrated by comparing it with other forms of sp2 carbons, including a graphene sheet, nanotubes, and an armchair-edged graphene nanoribbon.
TL;DR: A new type of fluorescence sensory material has been developed from an alkoxycarbonyl-substituted carbazole-cornered tetracycle, which facilitates long-range exciton migration and favors adsorption and diffusion of gaseous adsorbates within the film.
Abstract: A new type of fluorescence sensory material has been developed from an alkoxycarbonyl-substituted carbazole-cornered tetracycle Films fabricated from such materials are shown to be efficient in detecting explosive vapor, probably owing to the extended 1D molecular stacking between the component molecules and intrinsic nanoporous morphology thus formed within the film The former facilitates long-range exciton migration, while the latter favors adsorption and diffusion of gaseous adsorbates within the film A combination of these two characteristics enables efficient fluorescence quenching of the film by gaseous quenchers
TL;DR: An overview of the experimental advances is provided, the advantages and drawbacks of different techniques are discussed, and remaining issues are explored.
Abstract: What is the conductance of a single molecule? This basic and seemingly simple question has been a difficult one to answer for both experimentalists and theorists. To determine the conductance of a molecule, one must wire the molecule reliably to at least two electrodes. The conductance of the molecule thus depends not only on the intrinsic properties of the molecule, but also on the electrode materials. Furthermore, the conductance is sensitive to the atomiclevel details of the molecule-electrode contact and the local environment of the molecule. Creating identical contact geometries has been a challenging experimental problem, and the lack of atomiclevel structural information of the contacts makes it hard to compare calculations with measurements. Despite the difficulties, researchers have made substantial advances in recent years. This review provides an overview of the experimental advances, discusses the advantages and drawbacks of different techniques, and explores remaining issues.
TL;DR: In this article, a novel one-step synthesis of water soluble Au and Ag nanoparticles has been reported at room temperature using a naturally occurring bifunctional molecule, namely, gallic acid.
Abstract: A novel one step synthesis of water soluble Au and Ag nanoparticles has been reported at room temperature using a naturally occurring bifunctional molecule, namely, gallic acid. The mechanistic details of nanoparticle formation were elucidated by carrying out control experiments using a variety of model compounds. The newly synthesized nanoparticles are extremely stable in the pH range of 4.5−5.0, due to (i) the strong electrostatic interaction of the carboxylate anion of the capping agent with the surface of the nanoparticle and (ii) a very high ζ potential (−45 mV). Under these pH conditions, it is difficult to bring nanoparticles in proximity due to strong interparticle electrostatic repulsion. However, the unique coordination behavior of Pb2+ ions (coordination number up to 12, flexible bond length and geometry) allows the formation of a stable supramolecular complex resulting in plasmon coupling and a visual color change. Because of the rigid coordination geometry, other metal cations (Ca2+, Cu2+, Cd...
TL;DR: It is demonstrated that the intermolecular hydrogen bond C=O...H-O between fluorenone and methanol molecules is significantly strengthened in the electronically excited-state upon photoexcitation of the hydrogen-bonded FM-MeOH complex, which can be used to explain well all the spectral features of fluore None chromophore in alcoholic solvents.
Abstract: The time-dependent density functional theory (TDDFT) method was performed to investigate the excited-state hydrogen-bonding dynamics of fluorenone (FN) in hydrogen donating methanol (MeOH) solvent. The infrared spectra of the hydrogen-bonded FN-MeOH complex in both the ground state and the electronically excited states are calculated using the TDDFT method, since the ultrafast hydrogen-bonding dynamics can be investigated by monitoring the vibrational absorption spectra of some hydrogen-bonded groups in different electronic states. We demonstrated that the intermolecular hydrogen bond C=O...H-O between fluorenone and methanol molecules is significantly strengthened in the electronically excited-state upon photoexcitation of the hydrogen-bonded FM-MeOH complex. The hydrogen bond strengthening in electronically excited states can be used to explain well all the spectral features of fluorenone chromophore in alcoholic solvents. Furthermore, the radiationless deactivation via internal conversion (IC) can be facilitated by the hydrogen bond strengthening in the excited state. At the same time, quantum yields of the excited-state deactivation via fluorescence are correspondingly decreased. Therefore, the total fluorescence of fluorenone in polar protic solvents can be drastically quenched by hydrogen bonding.
TL;DR: It is found that junctions formed with dimethyl phosphine terminated alkanes have the highest conductance and this allows a detailed analysis of the single-molecule junction elongation properties which correlate well with calculations based on density functional theory.
Abstract: We compare the low bias conductance of a series of alkanes terminated on their ends with dimethyl phosphines, methyl sulfides, and amines and find that junctions formed with dimethyl phosphine terminated alkanes have the highest conductance. We see unambiguous conductance signatures with these link groups, indicating that the binding is well-defined and electronically selective. This allows a detailed analysis of the single-molecule junction elongation properties which correlate well with calculations based on density functional theory.
TL;DR: The molecules presented here provide a test-bed for competitive supramolecular chemistry, and on the basis of five crystal structures a ranking of the relative structural importance and influence of competing weak/ strong hydrogen bonds and weak/strong halogen bonds has been achieved.
Abstract: The molecules presented here provide a test-bed for competitive supramolecular chemistry, and on the basis of five crystal structures a ranking of the relative structural importance and influence of competing weak/strong hydrogen bonds and weak/strong halogen bonds has been achieved.
TL;DR: A review of the application of NMR to the measurement of the dissociation constants of protein-ligand complexes is given in this paper, where the authors discuss the available data treatments required to translate observed NMR effects into quantitative measurements of the stability of the complex in the form of dissociation constant (KD).
TL;DR: In this paper, the chemical origin of a set of complex organic molecules thought to be produced by grain surface chemistry in high mass young stellar objects (YSOs) was studied.
Abstract: Aims. We study the chemical origin of a set of complex organic molecules thought to be produced by grain surface chemistry in high mass young stellar objects (YSOs). Methods. A partial submillimeter line-survey was performed toward 7 high-mass YSOs aimed at detecting H 2 CO, CH 3 OH, CH 2 CO, CH 3 CHO, C 2 H 5 OH, HCOOH, HNCO and NH 2 CHO. In addition, lines of CH 3 CN. C 2 H 5 CN, CH 3 CCH, HCOOCH 3 , and CH 3 OCH 5 were observed. Rotation temperatures and beam-averaged column densities are determined. To correct for beam dilution and determine abundances for hot gas, the radius and H 2 column densities of gas at temperatures >100 K are computed using 850 μm dust continuum data and source luminosity. Results. Based on their rotation diagrams, molecules can be classified as either cold ( 100 K). This implies that complex organics are present in at least two distinct regions. Furthermore, the abundances of the hot oxygen-bearing species are correlated, as are those of HNCO and NH 2 CHO. This is suggestive of chemical relationships within, but not between, those two groups of molecules. Conclusions. The most likely explanation for the observed correlations of the various hot molecules is that they are "first generation" species that originate from solid-state chemistry. This includes H 2 CO, CH 3 OH, C 2 H 5 OH, HCOOCH 3 , CH 5 OCH 5 , HNCO, NH 2 CHO, and possibly CH 3 CN, and C 2 H 5 CN. The correlations between sources implies very similar conditions during their formation or very similar doses of energetic processing. Cold species such as CH 2 CO, CH 3 CHO, and HCOOH, some of which are seen as ices along the same lines of sight, are probably formed in the solid state as well, but appear to be destroyed at higher temperatures. A low level of non-thermal desorption by cosmic rays can explain their low rotation temperatures and relatively low abundances in the gas phase compared to the solid state. The CH 3 CCH abundances can be fully explained by low temperature gas phase chemistry. No cold N-containing molecules are found.
TL;DR: The proposed pair interaction energy decomposition analysis (PIEDA), redeveloped in the framework of the fragment molecular orbital method (FMO), can treat large molecular clusters and the systems in which fragments are connected by covalent bonds, such as proteins.
Abstract: The energy decomposition analysis (EDA) by Kitaura and Morokuma was redeveloped in the framework of the fragment molecular orbital method (FMO). The proposed pair interaction energy decomposition analysis (PIEDA) can treat large molecular clusters and the systems in which fragments are connected by covalent bonds, such as proteins. The interaction energy in PIEDA is divided into the same contributions as in EDA: the electrostatic, exchange-repulsion, and charge transfer energies, to which the correlation (dispersion) term was added. The careful comparison to the ab initio EDA interaction energies for water clusters with 2-16 molecules revealed that PIEDA has the error of at most 1.2 kcal/mol (or about 1%). The analysis was applied to (H2O)1024, the alpha helix, beta turn, and beta strand of polyalanine (ALA)10, as well as to the synthetic protein (PDB code 1L2Y) with 20 residues. The comparative aspects of the polypeptide isomer stability are discussed in detail.
TL;DR: It is demonstrated that disposable devices featuring both micro- and nanoscale features can greatly elongate DNA molecules when buffer conditions are controlled to alter DNA stiffness, and a complementary enzymatic labeling scheme is developed that tags specific sequences on elongated molecules within described nanoslit devices that are imaged via fluorescence resonance energy transfer.
Abstract: Molecular confinement offers new routes for arraying large DNA molecules, enabling single-molecule schemes aimed at the acquisition of sequence information. Such schemes can rapidly advance to become platforms capable of genome analysis if elements of a nascent system can be integrated at an early stage of development. Integrated strategies are needed for surmounting the stringent experimental requirements of nanoscale devices regarding fabrication, sample loading, biochemical labeling, and detection. We demonstrate that disposable devices featuring both micro- and nanoscale features can greatly elongate DNA molecules when buffer conditions are controlled to alter DNA stiffness. Furthermore, we present analytical calculations that describe this elongation. We also developed a complementary enzymatic labeling scheme that tags specific sequences on elongated molecules within described nanoslit devices that are imaged via fluorescence resonance energy transfer. Collectively, these developments enable scaleable molecular confinement approaches for genome analysis.