Conformations, vibrational frequencies and Raman intensities of short-chain fatty acid methyl esters using DFT with 6-31G(d) and Sadlej pVTZ basis sets

Density functional calculations, using B3LPY/6-31G(d) methods, have been used to investigate the conformations and vibrational (Raman) spectra of three short-chain fatty acid methyl esters (FAMEs) with the formula CnH2nO2 (n = 3-5). In all three FAMEs, the lowest energy conformer has a simple 'all-trans' structure but there are other conformers, with different torsions about the backbone, which lie reasonably close in energy to the global minimum. One result of this is that the solid samples we studied do not appear to consist entirely of the lowest energy conformer. Indeed, to account for the 'extra' bands that were observed in the Raman data but were not predicted for the all-trans conformer, it was necessary to add-in contributions from other conformers before a complete set of vibrational assignments could be made. Provided this was done, the agreement between experimental Raman frequencies and 6-31G(d) values (after scaling) was excellent, RSD = 12.6 cm(-1). However, the agreement between predicted and observed intensities was much less satisfactory. To confirm the validity of the approach followed by the 6-3 1 G(d) basis set, we used a larger basis set, Sadlej pVTZ, and found that these calculations gave accurate Raman intensities and simulated spectra (summed from two different conformers) that were in quantitative agreement with experiment. In addition, the unscaled Sadlej pVTZ, and the scaled 6-3 1 G(d) calculations gave the same vibrational mode assignments for all bands in the experimental data. This work provides the foundation for calculations on longer-chain FAMEs (which are closer to those found as triglycerides in edible fats and oils) because it shows that scaled 6-3 1 G(d) calculations give equally accurate frequency predictions, and the same vibrational mode assignments, as the much more CPU-expensive Sadlej pVTZ basis set calculations.

AMBIGUITIES IN ADSORBATE SITE ASSIGNMENT FROM VIBRATIONAL FREQUENCIES - A TLEED STRUCTURAL STUDY OF (2X1)CO-PD(110)

The structure of the (2 X 1)CO-Pd(110) surface phase has been determined by LEED intensity analysis. The CO molecule is found to be adsorbed in an atop site, tilted by 11-degrees +/- 4-degrees with respect to the surface normal, with a C-O bond length of 1.16 +/- 0.04 angstrom. Interestingly, the C-O vibrational frequency for this system (2003 cm-1) is virtually identical to the frequency observed for the (2 X 1)CO-Ni(110) surface phase (1998 cm-1) which a previous LEED study has shown involves bridge bound CO molecules. The result indicates that care must be taken in assigning site symmetries on the basis of C-O stretching frequencies alone.

A Density Functional Theory Study on the Active Center of Fe-Only Hydrogenase: Characterization and Electronic Structure of the Redox States

We have carried out extensive density functional theory (DFT) calculations for possible redox states of the active center in Fe-only hydrogenases. The active center is modeled by [(H(CH(3))S)(CO)(CN(-))Fe(p)(mu-DTN)(mu-CO)Fe(d)(CO)(CN(-))(L)](z) (z is the net charge in the complex; Fe(p)= the proximal Fe, Fe(d) = the distal Fe, DTN = (-SCH(2)NHCH(2)S-), L is the ligand that bonds with the Fed at the trans position to the bridging CO). Structures of possible redox states are optimized, and CO stretching frequencies are calculated. By a detailed comparison of all the calculated structures and the vibrational frequencies with the available experimental data, we find that (i) the fully oxidized, inactive state is an Fe(II)-Fe(II) state with a hydroxyl (OH(-)) group bonded at the Fe(d), (ii) the oxidized, active state is an Fe(II)-Fe(l) complex which is consistent with the assignment of Cao and Hall (J. Am. Chem. Soc. 2001, 123, 3734), and (iii) the fully reduced state is a mixture with the major component being a protonated Fe(l)-Fe(l) complex and the other component being its self-arranged form, Fe(II)-Fe(II) hydride, Our calculations also show that the exogenous CO can strongly bond with the Fe(II)-Fe(l) species, but cannot bond with the Fe(l)-Fe(l) complex. This result is consistent with experiments that CO tends to inhibit the oxidized, active state, but not the fully reduced state. The electronic structures of all the redox states have been analyzed. It is found that a frontier orbital which is a mixing state between the e(g) of Fe and the 2pi of the bridging CO plays a key role concerning the reactivity of Fe-only hydrogenases: (1) it is unoccupied in the fully oxidized, inactive state, half-occupied in the oxidized, active state, and fully occupied in the fully reduced state; (ii) the e(g)-2pi orbital is a bonding state, and this is the key reason for stability of the low oxidation states, such as Fe(l)-Fe(l) complexes; and (iii) in the e(g)-2pi orbital more charge accumulates between the bridging CO and the Fe(d) than between the bridging CO and the Fe(p), and the occupation increase in this orbital will enhance the bonding between the bridging CO and the Fe(d), leading to the bridging-CO shift toward the Fe(d).

Spectroscopy and metastability of CO22+ molecular ions

The spectroscopy and metastability of the carbon dioxide doubly charged ion, the CO22+ dication, have been studied with photoionization experiments: time-of-flight photoelectron photoelectron coincidence (TOF-PEPECO), threshold photoelectrons coincidence (TPEsCO), and threshold photoelectrons and ion coincidence (TPEsCO ion coincidence) spectroscopies. Vibrational structure is observed in TOF-PEPECO and TPEsCO spectra of the ground and first two excited states. The vibrational structure is dominated by the symmetric stretch except in the TPEsCO spectrum of the ground state where an antisymmetric stretch progression is observed. All three vibrational frequencies are deduced for the ground state and symmetric stretch and bending frequencies are deduced for the first two excited states. Some vibrational structure of higher electronic states is also observed. The threshold for double ionization of carbon dioxide is reported as 37.340+/-0.010 eV. The fragmentation of energy selected CO22+ ions has been investigated with TPEsCO ion coincidence spectroscopy. A band of metastable states from similar to38.7 to similar to41 eV above the ground state of neutral CO2 has been observed in the experimental time window of similar to0.1-2.3 mus with a tendency towards shorter lifetimes at higher energies. It is proposed that the metastability is due to slow spin forbidden conversion from bound excited singlet states to unbound continuum states of the triplet ground state. Another result of this investigation is the observation of CO++O+ formation in indirect dissociative double photoionization below the threshold for formation of CO22+. The threshold for CO++O+ formation is found to be 35.56+/-0.10 eV or lower, which is more than 2 eV lower than previous measurements. (C) 2005 American Institute of Physics.

Density functional and Monte Carlo studies of sulfur. I. Structure and bonding in S-n rings and chains (n=2-18) (vol 118, pg 9257, 2003)

Density functional calculations have been performed for ring isomers of sulfur with up to 18 atoms, and for chains with up to ten atoms. There are many isomers of both types, and the calculations predict the existence of new forms. Larger rings and chains are very flexible, with numerous local energy minima. Apart from a small, but consistent overestimate in the bond lengths, the results reproduce experimental structures where known. Calculations are also performed on the energy surfaces of S8 rings, on the interaction between a pair of such rings, and the reaction between one S8 ring and the triplet diradical S8 chain. The results for potential energies, vibrational frequencies, and reaction mechanisms in sulfur rings and chains provide essential ingredients for Monte Carlo simulations of the liquid–liquid phase transition. The results of these simulations will be presented in Part II.

Hydrogen bonding and collective proton modes in clusters and periodic layers of squaric acid: A density functional study

Hydrogen bonding in clusters and extended layers of squaric acid molecules has been investigated by density functional computations. Equilibrium geometries, harmonic vibrational frequencies, and energy barriers for proton transfer along hydrogen bonds have been determined using the Car-Parrinello method. The results provide crucial parameters for a first principles modeling of the potential energy surface, and highlight the role of collective modes in the low-energy proton dynamics. The importance of quantum effects in condensed squaric acid systems has been investigated, and shown to be negligible for the lowest-energy collective proton modes. This information provides a quantitative basis for improved atomistic models of the order-disorder and displacive transitions undergone by squaric acid crystals as a function of temperature and pressure. (C) 2001 American Institute of Physics.

Softened C-H modes of adsorbed methyl and their implications for dehydrogenation: An ab initio study

To investigate the softening of CH vibrational frequencies and their implications for dehydrogenation of adsorbed hydrocarbons, an issue of scientific and technological importance, density functional theory calculations have been performed on the chemisorption and dehydrogenation of CH3 on Cu(111) and Pt(111) surfaces. By comparing these results with those of Ni(111) we find that the CH bonds of the adsorbate, when close enough, interact with metal atoms of the surface. It is this interaction and its associated lengthening and weakening of CH bonds that is the physical origin of mode softening. We rule out the possibility of a relationship between the mere presence of mode softening and dehydrogenation. We do show, however, that there is a clear relationship between the extent to which a surface can induce mode softening and the activation energy to dehydrogenation. In addition, periodic trends concerning the extent of mode softening are reproduced. (C) 2001 American Institute of Physics.

Pterin detection using surface-enhanced Raman spectroscopy incorporating a straightforward silver colloid-based synthesis technique

Optical techniques toward the realization of sensitive and selective biosensing platforms have received considerable attention in recent times. Techniques based on interferometry, surface plasmon resonance, and waveguides have all proved popular, while spectroscopy in particular offers much potential. Raman spectroscopy is an information-rich technique in which the vibrational frequencies reveal much about the structure of a compound, but it is a weak process and offers poor sensitivity. In response to this problem, surface-enhanced Raman scattering (SERS) has received much attention, due to significant increases in sensitivity instigated by bringing the sample into contact with an enhancing substrate. Here we discuss a facile and rapid technique for the detection of pterins using SERS-active colloidal silver suspensions. Pterins are a family of biological compounds that are employed in nature in color pigmentation and as facilitators in metabolic pathways. In this work, small volumes of xanthopterin, isoxanthopterin, and 7,8-dihydrobiopterin have been examined while adsorbed to silver colloids. Limits of detection have been examined for both xanthopterin and isoxanthopterin using a 10-s exposure to a 12 mW 532 nm laser, which, while showing a trade-off between scan time and signal intensity, still provides the opportunity for the investigation of simultaneous detection of both pterins in solution. (C) 2011 Society of Photo-Optical Instrumentation Engineers (SPIE). [DOI: 10.1117/1.3600658]

Time-resolved resonance Raman scattering of triplet state anthracene in supercritical CO2

The first report of time-resolved resonance Raman (TR(3)) scattering in a supercritical fluid is presented. TR(3) spectra of the lowest triplet excited state (T-1) of anthracene in supercritical (SC) CO2 have been obtained over the pressure range 90-500 bar. These data have been complemented by conventional flash photolysis measurements of the excited state lifetime, transient absorbance difference, and fluorescence spectra over a similar pressure range. The spectroscopic data show systematic changes with increasing pressure; the Delta A spectra of the TI state recorded at two different temperatures display a red shift with increasing fluid pressure, which is in agreement with earlier work carried out over a smaller range of pressures. Similar shifts in the fluorescence are also observed. The vibrational frequencies of the T-1 state of anthracene are found to be relatively insensitive to applied pressure; indeed, the transient bands are readily identified by comparison with resonance Raman (RR) spectra of the T-1 state in cyclohexane solution. Small but well-defined shifts to lower cm(-1) with increasing pressure are observed in some of the vibrational bands of SC COE. The most marked change in the excited state Raman spectra is that the intensity of the T-1 anthracene features, relative to those of CO2, increases with applied pressure. The information which each of the above spectroscopic methods gives on the question of how pressure changes affect the structure and local environment of the excited state probe molecule in the SCF is discussed. Possible explanations for the observed increase in RR band intensities in terms of increased resonance Raman enhancement arising from the spectral shifts and/or the increased solubility of anthracene in CO2 with increasing pressure are also considered.

Nonconservative current-driven dynamics: beyond the nanoscale

Long metallic nanowires combine crucial factors for nonconservative current-driven atomic motion. These systems have degenerate vibrational frequencies, clustered about a Kohn anomaly in the dispersion relation, that can couple under current to form nonequilibrium modes of motion growing exponentially in time. Such motion is made possible by nonconservative current-induced forces on atoms, and we refer to it generically as the waterwheel effect. Here the connection between the waterwheel effect and the stimulated directional emission of phonons propagating along the electron flow is discussed in an intuitive manner. Nonadiabatic molecular dynamics show that waterwheel modes self-regulate by reducing the current and by populating modes in nearby frequency, leading to a dynamical steady state in which nonconservative forces are counter-balanced by the electronic friction. The waterwheel effect can be described by an appropriate effective nonequilibrium dynamical response matrix. We show that the current-induced parts of this matrix in metallic systems are long-ranged, especially at low bias. This nonlocality is essential for the characterisation of nonconservative atomic dynamics under current beyond the nanoscale.

Spectroscopy and metastability of CO 2 2+ molecular ions

The spectroscopy and metastability of the carbon dioxide doubly charged ion, the CO ₂ ²⁺ dication, have been studied with photoionization experiments: time-of-flight photoelectron photoelectron coincidence (TOF-PEPECO), threshold photoelectrons coincidence (TPEsCO), and threshold photoelectrons and ion coincidence (TPEsCO ion coincidence) spectroscopies. Vibrational structure is observed in TOF-PEPECO and TPEsCO spectra of the ground and first two excited states. The vibrational structure is dominated by the symmetric stretch except in the TPEsCO spectrum of the ground state where an antisymmetric stretch progression is observed. All three vibrational frequencies are deduced for the ground state and symmetric stretch and bending frequencies are deduced for the first two excited states. Some vibrational structure of higher electronic states is also observed. The threshold for double ionization of carbon dioxide is reported as 37.340±0.010 eV. The fragmentation of energy selected CO ₂ ²⁺ ions has been investigated with TPEsCO ion coincidence spectroscopy. A band of metastable states from ∼38.7 to ∼41 eV above the ground state of neutral CO ₂ has been observed in the experimental time window of ∼0.1-2.3 μs with a tendency towards shorter lifetimes at higher energies. It is proposed that the metastability is due to slow spin forbidden conversion from bound excited singlet states to unbound continuum states of the triplet ground state. Another result of this investigation is the observation of CO ⁺+O ⁺ formation in indirect dissociative double photoionization below the threshold for formation of CO ₂ ²⁺. The threshold for CO ⁺+O ⁺ formation is found to be 35.56±0.10 eV or lower, which is more than 2 eV lower than previous measurements.

Identification and bisection of temporal durations and tone frequencies: Common models for temporal and non-temporal stimuli.

Two experiments examined identification and bisection of tones varying in temporal duration (Experiment 1) or frequency (Experiment 2). Absolute identification of both durations and frequencies was influenced by prior stimuli and by stimulus distribution. Stimulus distribution influenced bisection for both stimulus types consistently, with more positively skewed distributions producing lower bisection points. The effect of distribution was greater when the ratio of the largest to smallest stimulus magnitude was greater. A simple mathematical model, temporal range frequency theory, was applied. It is concluded that (a) similar principles describe identification of temporal durations and other stimulus dimensions and (b) temporal bisection point shifts can be understood in terms of psychophysical principles independently developed in nontemporal domains, such as A. Parducci's (1965) range frequency theory.