Improved modification for the density-functional theory calculation of thermodynamic properties for C-H-O composite compounds

A three-parametric modification equation and the least-squares approach are adopted to calibrating hybrid density-functional theory energies of C(1)-C(10) straight-chain aldehydes, alcohols, and alkoxides to accurate enthalpies of formation DeltaH(f) and Gibbs free energies of formation DeltaG(f), respectively. All calculated energies of the C-H-O composite compounds were obtained based on B3LYP6-311++G(3df,2pd) single-point energies and the related thermal corrections of B3LYP6-31G(d,p) optimized geometries. This investigation revealed that all compounds had 0.05% average absolute relative error (ARE) for the atomization energies, with mean value of absolute error (MAE) of just 2.1 kJ/mol (0.5 kcal/mol) for the DeltaH(f) and 2.4 kJ/mol (0.6 kcal/mol) for the DeltaG(f) of formation.     

Bond energies and structures of ammonia-sulfuric acid positive cluster ions

New particle formation in the atmosphere is initiated by nucleation of gas-phase species. The small molecular clusters that act as seeds for new particles are stabilized by the incorporation of an ion. Ion-induced nucleation of molecular cluster ions containing sulfuric acid generates new particles in the background troposphere. The addition of a proton-accepting species to sulfuric acid cluster ions can further stabilize them and may promote nucleation under a wider range of conditions. To understand and accurately predict atmospheric nucleation, the stabilities of each molecular cluster within a chemical family must be known. We present the first comprehensive measurements of the ammonia-sulfuric acid positive ion cluster system NH(4)(+)(NH(3))(n)(H(2)SO(4))(s). Enthalpies and entropies of individual growth steps within this system were measured using either an ion flow reactor-mass spectrometer system under equilibrium conditions or by thermal decomposition of clusters in an ion trap mass spectrometer. Low level ab initio structural calculations provided inputs to a master equation model to determine bond energies from thermal decomposition measurements. Optimized ab initio structures for clusters up through n = 3, s = 3 are reported. Upon addition of ammonia and sulfuric acid pairs, internal proton transfer generates multiple NH(4)(+) and HSO(4)(-) ions within the clusters. These multiple-ion structures are up to 50 kcal mol(-1) more stable than corresponding isomers that retain neutral NH(3) and H(2)SO(4) species. The lowest energy n = s clusters are composed entirely of ions. The addition of acid-base pairs to the core NH(4)(+) ion generates nanocrystals that begin to resemble the ammonium bisulfate bulk crystal starting with the smallest n = s cluster, NH(4)(+)(NH(3))(1)(H(2)SO(4))(1). In the absence of water, this cluster ion system nucleates spontaneously for conditions that encompass most of the free troposphere.     

A quasichemical approach for protein-cluster free energies in dilute solution

Reversible formation of protein oligomers or small clusters is a key step in processes such as protein polymerization, fibril formation, and protein phase separation from dilute solution. A straightforward, statistical mechanical approach to accurately calculate cluster free energies in solution is presented using a cell-based, quasichemical (QC) approximation for the partition function of proteins in an implicit solvent. The inputs to the model are the protein potential of mean force (PMF) and the corresponding subcell degeneracies up to relatively low particle densities. The approach is tested using simple two and three dimensional lattice models in which proteins interact with either isotropic or anisotropic nearest-neighbor attractions. Comparison with direct Monte Carlo simulation shows that cluster probabilities and free energies of oligomer formation (DeltaG(i) (0)) are quantitatively predicted by the QC approach for protein volume fractions approximately 10(-2) (weight/volume concentration approximately 10 g l(-1)) and below. For small clusters, DeltaG(i) (0) depends weakly on the strength of short-ranged attractive interactions for most experimentally relevant values of the normalized osmotic second virial coefficient (b(2) (*)). For larger clusters (i"2), there is a small but non-negligible b(2) (*) dependence. The results suggest that nonspecific, hydrophobic attractions may not significantly stabilize prenuclei in processes such as non-native aggregation. Biased Monte Carlo methods are shown to accurately provide subcell degeneracies that are intractable to obtain analytically or by direct enumeration, and so offer a means to generalize the approach to mixtures and proteins with more complex PMFs.     

Effect of metal ions (Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+) and water coordination on the structure and properties of L-arginine and zwitterionic L-arginine

Interactions between metal ions and amino acids are common both in solution and in the gas phase. The effect of metal ions and water on the structure of L-arginine is examined. The effects of metal ions (Li(+), Na(+), K(+), Mg(2+), Ca(2+), Ni(2+), Cu(2+), and Zn(2+)) and water on structures of Arg x M(H2O)m , m = 0, 1 complexes have been determined theoretically by employing the density functional theories (DFT) and using extended basis sets. Of the three stable complexes investigated, the relative stability of the gas-phase complexes computed with DFT methods (with the exception of K(+) systems) suggests metallic complexes of the neutral L-arginine to be the most stable species. The calculations of monohydrated systems show that even one water molecule has a profound effect on the relative stability of individual complexes. Proton dissociation enthalpies and Gibbs energies of arginine in the presence of the metal cations Li(+), Na(+), K(+), Mg(2+), Ca(2+), Ni(2+), Cu(2+), and Zn(2+) were also computed. Its gas-phase acidity considerably increases upon chelation. Of the Lewis acids investigated, the strongest affinity to arginine is exhibited by the Cu(2+) cation. The computed Gibbs energies DeltaG(o) are negative, span a rather broad energy interval (from -150 to -1500 kJ/mol), and are appreciably lowered upon hydration.     

Temperature effects in mass spectrometry. Estimation of thermal energies of organic molecules

Thermal energies of gaseous organic molecules, relevant to unimolecular dissociations of odd- and even-electron ions, are estimated by ab initio/RRHO and empirical calculations. Thermal energies can be estimated with good accuracy by integration of molar heat capacities obtained from quadratic least-squares fits. Thermal energies in gaseous n-alkanes, alkanols, cholesterol, polyethylene glycols and oligopeptides are calculated and compared with estimates based on the equipartition principle.     

The molecular approach to heterogeneous nucleation

A molecular approach to heterogeneous nucleation has been developed. The expressions for the equilibrium cluster distribution, the reversible work of the cluster formation, and the nucleation rate have been derived. Two separate statements for the work of formation were formulated. If the equilibrium cluster distribution is normalized on the monomer concentration near the substrate surface, the reversible work of formation is expressed by DeltaG(het) (I) = (F(n) (het)-F(n) (hom))-(F(1) (het)-F(1) (hom)) + DeltaG(hom) where F(n) (het) and F(n) (hom) are the Helmholtz free energies of a cluster interacting with a substrate and a cluster not interacting with the substrate, respectively. If the equilibrium cluster distribution is normalized on the monomer concentration far from the substrate surface, the work of cluster formation is given by DeltaG(het) (II) = (F(n) (het)-F(n) (hom)) + DeltaG(hom). The former expression corresponds to the approach of the classical heterogeneous nucleation theory. The cluster partition function appears to be dependent on the location of a virtual plane, which separates the volume, where the interaction of the clusters with the substrate is effective from the one where interaction is negligible. Our Monte Carlo simulations have shown that the dependence is rather weak and thus the location of the plane is not very important. According to the simulations the variation of the plane position in the range from 20 to 50 Angstroms does not lead to a considerable change of the heterogeneous nucleation rate.     

Impact of different potentials on the structures and energies of clusters

Cluster studies have attracted much interest in the past decades because of their extraordinary properties. To describe the interaction between atoms or molecules and predict the energies and structures, potential functions are developed. However, different potentials generally produce different structures and energies for a cluster. To study the effect of potentials on the structure of a cluster, He clusters in the size range of 13-140 are investigated by Lennard-Jones (LJ), Pirani, and Hartree-Fock-dispersion individual damping (HFD-ID) potential with dynamic lattice searching (DLS) method. Potential function curves, cluster structures, bonds, and energies of the global minima are compared. The results show that cluster energies decrease with the values of the potential functions, the differences between structures depend upon the disagreements of the potentials, and the preferable motif of a cluster changes from icosahedron to decahedron with the increase of the derivative of the short-range part of the potentials.     

Ions in size-selected aqueous nanodrops: sequential water molecule binding energies and effects of water on ion fluorescence

The effects of water on ion fluorescence were investigated, and average sequential water molecule binding energies to hydrated ions, M(z)(H(2)O)(n), at large cluster size were measured using ion nanocalorimetry. Upon 248-nm excitation, nanodrops with ~25 or more water molecules that contain either rhodamine 590(+), rhodamine 640(+), or Ce(3+) emit a photon with average energies of approximately 548, 590, and 348 nm, respectively. These values are very close to the emission maxima of the corresponding ions in solution, indicating that the photophysical properties of these ions in the nanodrops approach those of the fully hydrated ions at relatively small cluster size. As occurs in solution, these ions in nanodrops with 8 or more water molecules fluoresce with a quantum yield of ~1. Ce(3+) containing nanodrops that also contain OH(-) fluoresce, whereas those with NO(3)(-) do not. This indirect fluorescence detection method has the advantages of high sensitivity, and both the size of the nanodrops as well as their constituents can be carefully controlled. For ions that do not fluoresce in solution, such as protonated tryptophan, full internal conversion of the absorbed 248-nm photon occurs, and the average sequential water molecule binding energies to the hydrated ions can be accurately obtained at large cluster sizes. The average sequential water molecule binding energies for TrpH(+)(H(2)O)(n) and a doubly protonated tripeptide, [KYK + 2H](2+)(H(2)O)(n), approach asymptotic values of ~9.3 (n ≥ 11) and ~10.0 kcal/mol (n ≥ 25), respectively, consistent with a liquidlike structure of water in these nanodrops.     

Aqueous solvation free energies of ions and ion-water clusters based on an accurate value for the absolute aqueous solvation free energy of the proton

Thermochemical cycles that involve pKa, gas-phase acidities, aqueous solvation free energies of neutral species, and gas-phase clustering free energies have been used with the cluster pair approximation to determine the absolute aqueous solvation free energy of the proton. The best value obtained in this work is in good agreement with the value reported by Tissandier et al. (Tissandier, M. D.; Cowen, K. A.; Feng, W. Y.; Gundlach, E.; Cohen, M. J.; Earhart, A. D.; Coe, J. V. J. Phys. Chem. A 1998, 102, 7787), who applied the cluster pair approximation to a less diverse and smaller data set of ions. We agree with previous workers who advocated the value of -265.9 kcal/mol for the absolute aqueous solvation free energy of the proton. Considering the uncertainties associated with the experimental gas-phase free energies of ions that are required to use the cluster pair approximation as well as analyses of various subsets of data, we estimate an uncertainty for the absolute aqueous solvation free energy of the proton of no less than 2 kcal/mol. Using a value of -265.9 kcal/mol for the absolute aqueous solvation free energy of the proton, we expand and update our previous compilation of absolute aqueous solvation free energies; this new data set contains conventional and absolute aqueous solvation free energies for 121 unclustered ions (not including the proton) and 147 conventional and absolute aqueous solvation free energies for 51 clustered ions containing from 1 to 6 water molecules. When tested against the same set of ions that was recently used to develop the SM6 continuum solvation model, SM6 retains its previously determined high accuracy; indeed, in most cases the mean unsigned error improves when it is tested against the more accurate reference data.     

Computation of hydration free energies of organic solutes with an implicit water model

A new approach for computing hydration free energies DeltaG(solv) of organic solutes is formulated and parameterized. The method combines a conventional PCM (polarizable continuum model) computation for the electrostatic component DeltaG(el) of DeltaG(solv) and a specially detailed algorithm for treating the complementary nonelectrostatic contributions (DeltaG(nel)). The novel features include the following: (a) two different cavities are used for treating DeltaG(el) and DeltaG(nel). For the latter case the cavity is larger and based on thermal atomic radii (i.e., slightly reduced van der Waals radii). (b) The cavitation component of DeltaG(nel) is taken to be proportional to the volume of the large cavity. (c) In the treatment of van der Waals interactions, all solute atoms are counted explicitly. The corresponding interaction energies are computed as integrals over the surface of the larger cavity; they are based on Lennard Jones (LJ) type potentials for individual solute atoms. The weighting coefficients of these LJ terms are considered as fitting parameters. Testing this method on a collection of 278 uncharged organic solutes gave satisfactory results. The average error (RMSD) between calculated and experimental free energy values varies between 0.15 and 0.5 kcal/mol for different classes of solutes. The larger deviations found for the case of oxygen compounds are probably due to a poor approximation of H-bonding in terms of LJ potentials. For the seven compounds with poorest fit to experiment, the error exceeds 1.5 kcal/mol; these outlier points were not included in the parameterization procedure. Several possible origins of these errors are discussed.     

Gibbs energies of formation of hydroxides of lanthanides and yttrium

The pH values of the formation of hydrates in solutions of yttrium(III), cerium(III), samarium(III), europium(III), erbium(III), and ytterbium(III) were determined by conductometric titration. The solubility products and Gibbs energies of formation for hydroxides for the elements listed were calculated. The average Gibbs energy of dissolution for lanthanide hydroxides was found to be approximately 149.83 ± 0.90 kJ/mol. The Gibbs energies of formation for hydroxides of the remaining lanthanides were assessed on this basis.     

Quantized hydration energies of ions and structure of hydration shell from the experimental gas-phase data

With previous data on alkali metal and halide ions included [Rais, J.; Okada, T. Anal. Sci. 2006, 22, 533], we analyzed rather broad data on ionic hydration from the point of view of gaseous cluster energetics. We have now added alkaline earth cations, Zn(2+), H(+), OH(-), Cu(+), Ag(+), Bi(+), Pb(+), and alkylammonium cations. The present analysis revealed the octa-coordinated nature of alkaline earth cations, which is not fully pronounced for Be(2+) and Zn(2+), existence of Eigen protonium complex, which is trigonally hydrated, and particular property of the first OH-, H(2)O cluster. Whereas these findings are generally in accordance with theoretical model calculation studies, we have foreseen in addition tetrahedral hydration for halide anions and Rb(+) and Cs(+), as well as for alkylammonium ions. The obtained picture of the quantized solvation of ions is mirrored in the ionization potentials of outer electrons of pertinent atoms. This is a second independent phenomenon, and together, they invoked a common pattern formation ("Aufbau") obeying tetra- and octa-coordinated principles.     

Equilibrium constants for dehydration of water adducts of aromatic carbon-carbon double bonds

Equilibrium constants (K(de)) are reported for the dehydration of hydrates of benzene, naphthalene, phenanthrene, and anthracene. Free energies of formation of the hydrates (DeltaG(o) (f)(aq)) are derived by combining free energies of formation of the parent (dihydroaromatic) hydrocarbon with estimates of the increment in free energy (DeltaG(OH)) accompanying replacement of a hydrogen atom of the hydrocarbon by a hydroxyl group. Combining these in turn with free energies of formation of H(2)O and of the aromatic hydrocarbon products furnishes the desired equilibrium constants. The method depends on the availability of thermodynamic data (i) for the hydrocarbons from which the hydrates are derived by hydroxyl substitution and (ii) for a sufficient range of alcohols to assess the structural dependence of DeltaG(OH). The data comprise chiefly heats of formation and standard entropies in the gas phase and free energies of transfer from the gas phase to aqueous solution (the latter being derived from vapor pressures and solubilities). They also include experimental measurements of equilibrium constants for dehydration of alcohols, especially cyclic, allylic, and benzylic alcohols. In general DeltaG(OH) depends on whether the alcohol is (a) primary, secondary, or tertiary; (b) allylic or benzylic; and (c) open chain or cyclic. Differences in geminal interactions of the hydroxyl group of the alcohol with alpha-alkyl and vinyl or phenyl groups account for variations in DeltaG(OH) of 5 kcal mol(-1). Weaker variations which arise from beta-vinyl/OH or beta-phenyl/OH interactions present in the aromatic hydrates but not in experimentally studied analogues are estimated as 1.0 kcal mol(-1). Equilibrium constants for dehydration may be expressed as their negative logs (pK(de)). Reactions yielding the following aliphatic, aromatic, and antiaromatic unsaturated products then have pK(de) values: +4.8, ethene; +15.0, ethyne; +22.1, cyclopropene; +28.4 cyclobutadiene; -22.2, benzene; -14.6, naphthalene; -9.2, phenanthrene; -7.4, anthracene. Large positive values are associated with formation of strained or antiaromatic double bonds and large negative values with aromatic double bonds. Trends in pK(de) parallel those of heats of hydrogenation. The results illustrate the usefulness of a substituent treatment for extending the range of currently available free energies of formation. In addition to hydroxyl substituent effects, DeltaG(OH), values of DeltaG(pi) for substitution of a pi-bond in a hydrocarbon are reported.     

Formation and emission of gold and silver carbide cluster ions in a single C60- surface impact at keV energies: experiment and calculations

Impact of fullerene ions (C(60)(-)) on a metallic surface at keV kinetic energies and under single collision conditions is used as an efficient way for generating gas phase carbide cluster ions of gold and silver, which were rarely explored before. Positively and negatively charged cluster ions, Au(n)C(m)(+) (n = 1-5, 1 ≤ m ≤ 12), Ag(n)C(m)(+) (n = 1-7, 1 ≤ m ≤ 7), Au(n)C(m)(-) (n = 1-5, 1 ≤ m ≤ 10), and Ag(n)C(m)(-) (n = 1-3, 1 ≤ m ≤ 6), were observed. The Au(3)C(2)(+) and Ag(3)C(2)(+) clusters are the most abundant cations in the corresponding mass spectra. Pronounced odd/even intensity alternations were observed for nearly all Au(n)C(m)(+/-) and Ag(n)C(m)(+/-) series. The time dependence of signal intensity for selected positive ions was measured over a broad range of C(60)(-) impact energies and fluxes. A few orders of magnitude immediate signal jump instantaneous with the C(60)(-) ion beam opening was observed, followed by a nearly constant plateau. It is concluded that the overall process of the fullerene collision and formation∕ejection of the carbidic species can be described as a single impact event where the shattering of the incoming C(60)(-) ion into small C(m) fragments occurs nearly instantaneously with the (multiple) pickup of metal atoms and resulting emission of the carbide clusters. Density functional theory calculations showed that the most stable configuration of the Au(n)C(m)(+) (n = 1, 2) clusters is a linear carbon chain with one or two terminal gold atoms correspondingly (except for a bent configuration of Au(2)C(+)). The calculated AuC(m) adiabatic ionization energies showed parity alternations in agreement with the measured intensity alternations of the corresponding ions. The Au(3)C(2)(+) ion possesses a basic Au(2)C(2) acetylide structure with a π-coordinated third gold atom, forming a π-complex structure of the type [Au(π-Au(2)C(2))](+). The calculation shows meaningful contributions of direct gold-gold bonding to the overall stability of the Au(3)C(2)(+) complex.     

Single-ion solvation free energies and the normal hydrogen electrode potential in methanol, acetonitrile, and dimethyl sulfoxide

The division of thermodynamic solvation free energies of electrolytes into contributions from individual ionic constituents is conventionally accomplished by using the single-ion solvation free energy of one reference ion, conventionally the proton, to set the single-ion scales. Thus, the determination of the free energy of solvation of the proton in various solvents is a fundamental issue of central importance in solution chemistry. In the present article, relative solvation free energies of ions and ion-solvent clusters in methanol, acetonitrile, and dimethyl sulfoxide (DMSO) have been determined using a combination of experimental and theoretical gas-phase free energies of formation, solution-phase reduction potentials and acid dissociation constants, and gas-phase clustering free energies. Applying the cluster pair approximation to differences between these relative solvation free energies leads to values of -263.5, -260.2, and -273.3 kcal/mol for the absolute solvation free energy of the proton in methanol, acetonitrile, and DMSO, respectively. The final absolute proton solvation free energies are used to assign absolute values for the normal hydrogen electrode potential and the solvation free energies of other single ions in the solvents mentioned above.     

Gas-phase reactions of carbon dioxide with atomic transition-metal and main-group cations: room-temperature kinetics and periodicities in reactivity

The chemistry of carbon dioxide has been surveyed systematically with 46 atomic cations at room temperature using an inductively-coupled plasma/selected-ion flow tube (ICP/SIFT) tandem mass spectrometer. The atomic cations were produced at ca. 5500 K in an ICP source and allowed to cool radiatively and to thermalize by collisions with Ar and He atoms prior to reaction downstream in a flow tube in helium buffer gas at 0.35 +/- 0.01 Torr and 295 +/- 2 K. Rate coefficients and products were measured for the reactions of first-row atomic ions from K(+) to Se(+), of second-row atomic ions from Rb(+) to Te(+) (excluding Tc(+)), and of third-row atomic ions from Cs(+) to Bi(+). CO(2) was found to react in a bimolecular fashion by O atom transfer only with 9 early transition-metal cations: the group 3 cations Sc(+), Y(+), and La(+), the group 4 cations Ti(+), Zr(+), and Hf(+), the group 5 cations Nb(+) and Ta(+), and the group 6 cation W(+). Electron spin conservation was observed to control the kinetics of O atom transfer. Addition of CO(2) was observed for the remaining 37 cations. While the rate of addition was not measurable some insight was obtained into the standard free energy change, DeltaG(o), for CO(2) ligation from equilibrium constant measurements. A periodic variation in DeltaG(o) was observed for first row cations that is consistent with previous calculations of bond energies D(0)(M(+)-CO(2)). The observed trends in D(0) and DeltaG(o) are expected from the variation in electrostatic attraction between M(+) and CO(2) which follows the trend in atomic-ion size and the trend in repulsion between the orbitals of the atomic cations and the occupied orbitals of CO(2). Higher-order CO(2) cluster ions with up to four CO(2) ligands also were observed for 24 of the atomic cations while MO(2)(+) dioxide formation by sequential O atom transfer was seen only with Hf(+), Nb(+), Ta(+), and W(+).     

Measurement of real free energies of transfer of individual ions from water to other solvents with the jet cell

Resolution of the activities of solutions of electrolytes into the individual ionic contributions cannot be carried out rigorously and requires the introduction of extrathermodynamic assumptions which have inherent uncertainties. The most commonly used approaches are basically similar in that they are based on the assumed solvent independence of the difference in the enthalpy or Gibbs energy of transfer of pairs of model solutes, e.g., tetraphenylarsonium and tetraphenylborate ions, or ferricinium ion and ferrocene. In this work we follow an alternative approach pioneered by Parsons involving measurement in the jet (Kenrick) cell of outer-potential differences between solutions of the same electrolyte in two solvents. These potential differences provide the real free energies of transfer of individual ions which, in turn, differ from the usual Gibbs energies of transfer by the work required to transfer the ion through the dipolar layers at the two solvent-gas interfaces. One objective of this work was to improve the reliability of real free energy of transfer measurements, which are experimentally demanding, to within ca. ±0.5 kJ-mol^–1 in order to match typical uncertainties in Gibbs transfer energies of electrolytes. This goal was met, in most instances, by careful evaluation of experimental parameters (particularly jet pressure). A major improvement over previous measurements was made by adding a supporting electrolyte which allowed stable potentials to be obtained at test electrolyte concentrations as low as 10^–4M. Real free energy changes are reported for the transfer of silver ion from water to methanol, ethanol, acetonitrile, propylene carbonate and dimethyl sulfoxide, as well as for the transfer of chloride ion from water to methanol and ethanol. Reliable data of this kind may lead to improved understanding of either the properties of the surfaces of solvents or the interactions of model solutes with solvents, depending on which of the two fields develops most.     

Guided ion beam studies of the reactions of Co n+ (n=1-18) with N2: Cobalt cluster mononitride and dinitride bond energies

The reactions of Co n+ (n=1-18) with N2 are measured as a function of kinetic energy over a range of 0-15 eV in a guided ion beam tandem mass spectrometer. A variety of Co m +, Co m N+, and Co m N2+ (m相似文献   

Binding energies of CO on gold cluster cations Au n + (n=1-65): a radiative association kinetics study

Room temperature CO adsorption on isolated gold cluster cations is studied over a wide size range (Au(n) (+),126), with notable exceptions at n=30, 31 and 48, 49 which manifest local binding energy maxima. For the smallest sizes (3相似文献