Standard State Enthalpies Research Articles

Entropic origin of Mg 2+ -facilitated RNA folding

Mg(2+) is essential for the proper folding and function of RNA, though the effect of Mg(2+) concentration on the free energy, enthalpy, and entropy landscapes of RNA folding is unknown. This work exploits temperature-controlled single-molecule FRET methods to address the thermodynamics of RNA folding pathways by probing the intramolecular docking/undocking kinetics of the ubiquitous GAAA tetraloop-receptor tertiary interaction as a function of [Mg(2+)]. These measurements yield the barrier and standard state enthalpies, entropies, and free energies for an RNA tertiary transition, in particular, revealing the thermodynamic origin of [Mg(2+)]-facilitated folding. Surprisingly, these studies reveal that increasing [Mg(2+)] promotes tetraloop-receptor interaction by reducing the entropic barrier (-TΔS(++)(dock)) and the overall entropic penalty (-TΔS(+) (dock)) for docking, with essentially negligible effects on both the activation enthalpy (ΔH(++)(dock)) and overall exothermicity (ΔH(+)(dock)). These observations contrast with the conventional notion that increasing [Mg(2+)] facilitates folding by minimizing electrostatic repulsion of opposing RNA helices, which would incorrectly predict a decrease in ΔH(++)(dock)) and ΔH(+)(dock)) with [Mg(2+)]. Instead we propose that higher [Mg(2+)] can aid RNA folding by decreasing the entropic penalty of counterion uptake and by reducing disorder of the unfolded conformational ensemble.

Adsorption of Water Molecules on Selected Charged Sodium–Chloride Clusters

The adsorption of water molecules (H(2)O) on sodium chloride cluster cations and anions was studied at 298 K over a mass range of 100-1200 amu using a custom-built laser desorption ionization reactor and mass spectrometer. Under the conditions used, the cations Na(3)Cl(2)(+) and Na(4)Cl(3)(+) bind up to three water molecules, whereas the larger cations, Na(5)Cl(4)(+) to Na(19)Cl(18)(+), formed hydrates with one or two only. The overall trend is a decrease in hydration with increasing cluster size, with an abrupt drop occurring at the closed-shell Na(14)Cl(13)(+). As compared to the cluster cations, the cluster anions showed almost no adsorption. Among smaller clusters, a weak adsorption of one water molecule was observed for the cluster anions Na(6)Cl(7)(-) and Na(7)Cl(8)(-). In the higher mass region, a substantial adsorption of one water molecule was observed for Na(14)Cl(15)(-). Density functional theory (DFT) computations were carried out for the adsorption of one molecule of H(2)O on the cations Na(n)Cl(n-1)(+), for n = 2-8, and the anions Na(n)Cl(n+1)(-), for n = 1-7. For each ion, the structure of the hydrate, the hydration energy, and the standard-state enthalpy, entropy, and Gibbs energy of hydration at 298 K were computed. In addition, it was useful to compute the distortion energy, defined as the electronic energy lost due to weakening of the Na-Cl bonds upon adsorption of H(2)O. The results show that strong adsorption of a H(2)O molecule occurs for the linear cations only at an end Na ion and for the nonlinear cations only at a corner Na ion bonded to two Cl ions. An unexpected result of the theoretical investigation for the anions is that certain low-energy isomers of Na(6)Cl(7)(-) and Na(7)Cl(8)(-) bind H(2)O strongly enough to produce the observed weak adsorption. The possible implications of these results for the initial hydration of extended NaCl surfaces are discussed.

A thermodynamic framework for understanding temperature sensing by transient receptor potential (TRP) channels

The exceptionally high temperature sensitivity of certain transient receptor potential (TRP) family ion channels is the molecular basis of hot and cold sensation in sensory neurons. The laws of thermodynamics dictate that opening of these specialized TRP channels must involve an unusually large conformational standard-state enthalpy, ΔH o : positive ΔH o for heat-activated and negative ΔH o for cold-activated TRPs. However, the molecular source of such high-enthalpy changes has eluded neurobiologists and biophysicists. Here we offer a general, unifying mechanism for both hot and cold activation that recalls long-appreciated principles of protein folding. We suggest that TRP channel gating is accompanied by large changes in molar heat capacity, ΔC P . This postulate, along with the laws of thermodynamics and independent of mechanistic detail, leads to the conclusion that hot- and cold-sensing TRPs operate by identical conformational changes.

Survey of main group compounds (H [sbnd]Br) at the Gaussian-4 level of theory: Adiabatic ionization energies and enthalpies of formation

Gas phase adiabatic ionization energies (AIEs) and standard state (298.15 K, 1 atm) enthalpies of formation Δ f H ( g ) ° were calculated at the Gaussian-4 (G4) level of theory for a suite of 319 and 398 main group compounds, respectively, containing the elements hydrogen through bromine. National Institute of Standards and Technology (NIST) evaluated AIEs were available for comparison with 44 compounds, yielding good agreement when the significant variability among the individual experimental reports was taken into consideration. AIEs were estimated at the G4 level of theory for a further 126 main group compounds having at least one experimental datapoint in the NIST database, but not a NIST evaluated AIE, as well as 149 main group compounds without any experimental data in the NIST database. Experimental Δ f H ( g ) ° were available for comparison with 144 compounds, yielding good agreement, particularly against compounds with evaluated Δ f H ( g ) ° . Δ f H ( g ) ° were estimated at the G4 level of theory for a further 254 main group compounds without any experimental data. The datasets comprise a benchmark set of theoretical data against which to assess future experimental and theoretical results.

Comments on “Estimated Gas-Phase Standard State Enthalpies of Formation for Organic Compounds Using the Gaussian-4 (G4) and W1BD Theoretical Methods” (Rayne, S.; Forest, K.J. Chem. Eng. Data2010,55, 5359−5364)

ADVERTISEMENT RETURN TO ISSUEPREVComment/ReplyNEXTComments on “Estimated Gas-Phase Standard State Enthalpies of Formation for Organic Compounds Using the Gaussian-4 (G4) and W1BD Theoretical Methods” (Rayne, S.; Forest, K. J. Chem. Eng. Data2010, 55, 5359−5364)Olga V. Dorofeeva*View Author Information Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia*E-mail: [email protected]Cite this: J. Chem. Eng. Data 2011, 56, 3, 682–683Publication Date (Web):February 22, 2011Publication History Received10 December 2010Accepted28 January 2011Published online22 February 2011Published inissue 10 March 2011https://doi.org/10.1021/je101305cCopyright © 2011 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views348Altmetric-Citations3LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (701 KB) Get e-AlertsSUBJECTS:Aromatic compounds,Chemical calculations,Enthalpy,Hydrocarbons,Molecular structure Get e-Alerts

Association of ionic liquids in solution: a combined dielectric and conductivity study of [bmim][Cl] in water and in acetonitrile

Ion association of the ionic liquid [bmim][Cl] in acetonitrile and in water was studied by dielectric spectroscopy for salt concentrations c ≤ 1.3 M at 298.15 K and by measurement of molar electrical conductivities, Λ, of dilute solutions (c ≤ 0.006 M) in the temperature range 273.15 ≲ T/K ≤ 313.15. Whilst acetonitrile solutions of [bmim][Cl] exhibit moderate ion pairing, with an association constant of K°(A) ≈ 60 M(-1) and increasing with temperature, [bmim][Cl] is only weakly associated in water (K°(A) ≈ 6 M(-1)) and ion pairing decreases with rising temperature. Only contact ion pairs were detected in both solvents. Standard-state enthalpy, entropy and heat capacity changes of ion association were derived, as well as the activation enthalpy of charge transport and the limiting conductivity of the cation, λ(∞) ([bmim](+)). These data, in conjunction with effective solvation numbers obtained from the dielectric spectra, suggest that the solvation of [bmim](+) is much weaker in water than in acetonitrile.

Estimated Gas-Phase Standard State Enthalpies of Formation for Organic Compounds Using the Gaussian-4 (G4) and W1BD Theoretical Methods

Gas-phase standard state (298.15 K, 1.01325 bar [1 atm]) enthalpies of formation (ΔfH°(g)) were calculated using the atomization approach for 313 organic compounds with the Gaussian-4 (G4) composite method and for 54 molecules with the W1BD level of theory. The functional group types considered span a range of mono- and polyfunctionalized halogenated, saturated and unsaturated, cyclic and acyclic, and heteroatom (N, O, S) substituted moieties without substantial conformational complexity. Good agreement was found using both computational methods against available experimental data.

Gas-phase enthalpies of formation, acidities, and strain energies of the [m, n]polyprismanes (m ≥ 2; n = 3–8; m × n ≤ 16): a CBS-Q//B3, G4MP2, and G4 theoretical study

Gas-phase standard state (298.15 K, 1 atm) enthalpies of formation (ΔfH(g)o) and enthalpies (ΔacidH(g)o) and free energies (ΔacidG(g)o) of acid dissociation were calculated for the [m, n]polyprismanes (m ≥ 2; n = 3–8; m × n ≤ 16) using the composite method CBS-Q//B3, G4MP2, and G4 levels of theory. Excellent agreement was obtained between the theoretical estimates and experimental values for [2, 4]polyprismane (cubane), the only member with reliable experimental data. Gas-phase acidities of the [2, 3], [2, 4], and [2, 5]polyprismanes correlate well with percent s-character of the C–H bonds as determined by nuclear magnetic resonance spectroscopy. Based on this correlation, and calculations on the [2, n] (n = 3–8) series, no substantial change in the gas-phase acidity or C–H bond s-character is expected with increasing [2,n]polyprismane ring size at n = 6–8. Where three or more stacked [m, n]polyprismane rings are present (m > 2), geometry optimizations for the deprotonated anions converged on cage-opened non-prismatic geometries, suggesting these compounds may be structurally unstable to gas-phase deprotonation/protonation cycles and potentially preventing reliable experimental measurement or calculation of their acidities. Total strain energies (Estr) increase with larger [m, n]polyprismane size, and strain energies per one C–C bond (EstrCC) increase with increasing stack height within a given ring size series. Within a given stack height, EstrCC reaches a minimum with a ring size of five, increasing with either decreasing or increasing ring size away from this minima. Estr and EstrCC do not correlate with gas-phase acidity, likely because the deprotonated anionic [2, n]polyprismane geometry retains approximately equal strain as the undissociated species despite substantial geometry changes due to carbon acid dissociation.

Gas phase acidities and associated equilibrium isotope effects for selected main group mono- and polyhydrides, carbon acids, and oxyacids: A G4 and W1BD study

Gas phase standard state (298.15 K, 1 atm) enthalpies (Δ acid H° (g)) and free energies (Δ acid G° (g)) of acid dissociation were calculated at the Gaussian-4 (G4) and W1BD levels of theory for a range of perproteated, perdeuterated, pertritiated, and partially isotopically labeled main group mono- and polyhydrides, carbon acids, and oxyacids. Excellent agreement was obtained between the available experimental datasets and the theoretical estimates, with effectively equivalent Δ acid H° (g)/Δ acid G° (g) prediction accuracy for the G4 and W1BD methods on carbon acids and oxyacids. The W1BD level of theory provided Δ acid H° (g)/Δ acid G° (g) errors about one-half those of the G4 method on main group hydrides. G4 and W1BD predicted primary and secondary equilibrium isotope effects (EIEs) on gas phase acidity for deuterium and tritium substitution exhibit periodic trends among the main group hydrides, as well as acid strength and structure–property relationships for some groups of carbon acids and oxyacids. Primary EIEs calculated at the W1BD level for various isotopologues of the H 2, LiH, CH 4, NH 3, SiH 4, SH 2, and ClH main group hydrides using the major isotopes for each non-protic element declined in magnitude with increasing atomic number due to decreasing mass differences between the respective isotopologues.

Performance of Gaussian-3 and Gaussian-4 level theoretical methods in estimating gas phase enthalpies of formation for representative [formula omitted] and [formula omitted] chlorofluorocarbons and hydrochlorofluorocarbons

The Gaussian-3 (G3) and Gaussian-4 (G4) ab initio post-Hartree–Fock composite methods were employed to estimate the gas phase standard state (298.15 K, 1 atm) enthalpies of formation ( Δ f H ( g ) ∘ ) for 38 representative C 1 ( n = 15 ) and C 2 ( n = 23 ) chlorofluorocarbons (CFCs) and hydrochlorofluorocarbons (HCFCs). Using the atomization approach, good agreement was found between experimental Δ f H ( g ) ∘ and corresponding G3 and G4 estimates. Where significant differences between G3/G4 and experimental Δ f H ( g ) ∘ exist, the errors may be due to problems with the experimental data rather than deficiencies in the theoretical methods.

Thermodynamic Properties of Autunite, Uranyl Hydrogen Phosphate, and Uranyl Orthophosphate from Solubility and Calorimetric Measurements

In this study, we use solubility and drop-solution calorimetry measurements to determine the thermodynamic properties of the uranyl phosphate phases autunite, uranyl hydrogen phosphate, and uranyl orthophosphate. Conducting the solubility measurements from both supersaturated and undersaturated conditions and under different pH conditions rigorously demonstrates attainment of equilibrium and yields well-constrained solubility product values. We use the solubility data and the calorimetry data, respectively, to calculate standard-state Gibbs free energies of formation and standard-state enthalpies of formation for these uranyl phosphate phases. Combining these results allows us also to calculate the standard-state entropy of formation for each mineral phase. The results from this study are part of a combined effort to develop reliable and internally consistent thermodynamic data for environmentally relevant uranyl minerals. Data such as these are required to optimize and quantitatively assess the effect of phosphate amendment remediation technologies for uranium contaminated systems.

Manganese Borohydride As a Hydrogen-Storage Candidate: First-Principles Crystal Structure and Thermodynamic Properties

Manganese borohydride (Mn(BH4)2) is considered to be a high-capacity (∼10 wt %) solid-state hydrogen storage candidate, but so far has not been shown to exhibit reversible hydrogenation. This study presents the calculated crystal structure and electronic structure of Mn(BH4)2 from density-functional theory within the generalized gradient approximation and thermodynamic properties from the direct method lattice dynamics. A thermodynamically stable phase of Mn(BH4)2 is identified. The calculation of Gibbs energy at finite temperatures suggests that the stable phase is of I4̅m2 symmetry. The formation energy of Mn(BH4)2 for the I4̅m2 symmetry solid is −28.93 kJ/f.u. at 0 K including zero-point energy corrections, and the standard state enthalpy of formation is predicted to be −58.89 kJ/f.u. The most feasible dehydrogenation reaction is found to be Mn(BH4)2 = Mn + 2B+ 4H2, which is an endothermic reaction at decomposition temperature. The spin-polarized electronic density of states shows that manganese borohydride has a half-metallic nature due to the presence of half-filled 3d electrons from Mn. The electronic structure calculations and analysis show that the interaction between Mn atoms and BH4 complexes has an ionic character, while the internal bonding of BH4 is essentially covalent.

Standard state thermodynamic properties of aqueous cesium chloride using high dilution calorimetry up to 598.15 K

In this communication we report the calorimetric data for the standard state enthalpies of solution of cesium chloride obtained from low concentrations, down to (10 −3 m), integral heats of solution measurement up to temperature of 573.30 K and extrapolated to 598.15 K. From these data and the unified theory of electrolytes, the complete standard state thermodynamic properties ( H 2 ∘ , G 2 ∘ , C p , 2 ∘ , V 2 ∘ , ( ∂ V 2 ∘ / ∂ T ) p , ( ∂ V 2 ∘ / ∂ p ) T ) of aqueous cesium chloride were determined up to temperature of 598.15 K.

Standard State Thermodynamic Properties of Aqueous Sodium Chloride Using High Dilution Calorimetry at Extreme Temperatures and Pressures

In this communication, we report the first calorimetric data for the standard state enthalpies of a solution of sodium chloride obtained from high dilution, down to (10(-3) m), integral heats of solution measurements to 596.30 K. Although there are no comparable thermodynamic data available at such high dilutions in the literature, the present results for NaCl(aq) can be used for many thermodynamic studies by others to achieve a complete thermodynamic description of this key electrolyte over very wide ranges of concentration. From the recently developed unified theory of electrolytes, the experimental data from this study were used to predict Gibbs free energies of hydration of sodium chloride up to 1100 K. These Gibbs free energies of hydration at different pressures and densities compare well with reported values obtained from ab initio calculations by others.

The standard state thermodynamic properties for completely ionized hydrochloric acid and ionization of water up to 523 K

In this communication we report calorimetric data for the standard state enthalpies of solution of α-Ba(OH) 2 in high dilution (10 −3 m) hydrochloric acid obtained from integral heats of solution measurements from temperatures of (333.55 to 516.64) K and extrapolated to 298.15 K. From previous studies in this laboratory on BaCl 2(aq) and auxiliary literature data, the standard state thermodynamic functions for completely ionized HCl(aq) can be determined. These new data are in good agreement and confirm our previously reported results on HCl(aq) from ionic additivity. The enthalpy of formation of solid α-Ba(OH) 2 at temperature of 298.15 K of −939.38 kJ · mol −1 can also be calculated from the present results. Values of the standard state heat capacity change for the ionization of water up to temperature of 523.15 K and at p sat were calculated from present results using the literature data for NaOH(aq) and NaCl(aq) obtained from high dilution calorimetric measurements.

Solubility measurements of the uranyl oxide hydrate phases metaschoepite, compreignacite, Na–compreignacite, becquerelite, and clarkeite

The mobility of uranium under oxidizing conditions can only be modeled if the thermodynamic stabilities of the secondary uranyl minerals are known. Toward this end, we synthesized metaschoepite (UO 3(H 2O) 2), becquerelite (Ca(UO 2) 6O 4(OH) 6(H 2O) 8), compreignacite (K 2(UO 2) 6O 4(OH) 6(H 2O) 7), sodium compreignacite (Na 2(UO 2) 6O 4(OH) 6(H 2O) 7), and clarkeite (Na(UO 2)O(OH)) and performed solubility measurements from both undersaturation and supersaturation under controlled-pH conditions. The solubility measurements rigorously constrain the values of the solubility products for these synthetic phases, and consequently the standard-state Gibbs free energies of formation of the phases. The calculated lg solubility product values (lg K sp), with associated 1 σ uncertainties, for metaschoepite, becquerelite, compreignacite, sodium compreignacite, and clarkeite are (5.6 −0.2/+0.1), (40.5 −1.4/+0.2), (35.8 −0.5/+0.3), (39.4 −1.1/+0.7), and (9.4 −0.9/+0.6), respectively. The standard-state Gibbs free energies of formation, with their 2 σ uncertainties, for these same phases are (−1632.2 ± 7.4) kJ · mol −1, (−10305.6 ± 26.5) kJ · mol −1, (−10107.3 ± 21.8) kJ · mol −1, (−10045.6 ±24.5) kJ · mol −1, and (−1635.1 ± 23.4) kJ · mol −1, respectively. Combining our data with previously measured standard-state enthalpies of formation for metaschoepite, becquerelite, sodium compreignacite, and clarkeite yields calculated standard-state entropies of formation, with associated 2 σ uncertainties, of (−532.5 ± 8.1) J · mol −1 · K −1, (−3634.5 ± 29.7) J · mol −1 · K −1, ( −2987.6 ± 28.5) J · mol −1 · K −1, and (−300.5 ± 23.9) J · mol −1 · K −1, respectively. The measurements and associated calculated thermodynamic properties from this study not only describe the stability and solubility at T = 298 K, but also can be used in predictions of uranium mobility through extrapolation of these properties to temperatures and pressures of geologic and environmental interest.

４f電子雲拡大系列：Ln(III)化合物熱化学データの四組効果とRSPＥT式から求められるラカー・パラメ－ターの大小関係

４f電子雲拡大系列：Ln(III)化合物熱化学データの四組効果とRSPＥT式から求められるラカー・パラメ－ターの大小関係

Computational Methods in Organic Thermochemistry. 2. Enthalpies and Free Energies of Formation for Functional Derivatives of Organic Hydrocarbons

Standard state enthalpies and free energies of formation for nitrogen-, oxygen-, sulfur-, fluorine-, chlorine-, and silicon-containing compounds can be computed with reasonable accuracy (usually within four and often two kJ/mol) using the G3 and G3MP2 model chemistries. In several of the families, compounds with as many as 10 carbon atoms have been computed. Larger errors are found in the free energies of these longer chain molecules which can be reduced by compensating for the presence of multiple conformers having a significant population at 298.15 K. In some instances, those substances showing large deviations are found to have experimental energies that may be erroneous.

Gas phase thermodynamic properties of PBDEs, PBBs, PBPs, HBCD and TBBPA predicted using DFT method

The gas phase thermodynamic properties of 209 polybrominated diphenyl ethers (PBDEs), 209 polybrominated biphenyls (PBBs), 19 polybrominated phenols (PBPs), hexabromocyclododecane (HBCD) and tetrabromobisphenol A (TBBPA), including standard state entropy ( S ∘), heat capacity ( C p), enthalpy ( Δ H f ∘ ) and Gibbs free energy of formation ( Δ G f ∘ ) , were predicted using a combination of quantum mechanical computations performed using the Gaussian 03 program at the B3LYP/6-31G(d) level, and thermodynamic relationships derived from the law of energy conservation. The obtained results showed a strong influence of the bromine substitution pattern on the thermodynamic properties of the compounds. For instance, the thermodynamic stability of all congeners decreases with increasing number of Br atoms, especially if substituted at ortho < meta < para positions. Taking into account differences in the Gibbs free energy of formation, the most and least stable congeners in each isomer group were determined. Application of the obtained results in the thermodynamic analysis of the reported experimental stabilities of the compounds afforded the following conclusions: (i) the order of decreasing stability of the PBDEs calculated in this study is in good agreement with the increasing rate of their photochemical degradation; (ii) the formations of lower brominated polybrominated dibenzofurans (PBDFs) instead of adequate congeners of PBDEs during the photolytic debromination of decabromodiphenyl ether (DeBDE) seemed to be thermodynamically favored; (iii) the debromination of PBDEs does not follow just one thermodynamic path, but is rather multidirectional, leading to a mixture of several congeners, the concentration of which is related to their thermodynamic stability.

Computational Methods in Organic Thermochemistry. 1. Hydrocarbon Enthalpies and Free Energies of Formation

Standard state enthalpies and free energies of formation can be computed with reasonable accuracy (usually within 4 and often 2 kJ/mol) using high level model chemistries. A comparison set of nearly 300 organic compounds ranging from 1 to 10 carbon atoms having a variety of functional groups for which enthalpy and free energy literature values are available has been examined using G2, G2MP2, G3, G3MP2, G3B3, G3MP2B3, CBS-QB3, and density functional (B3LYP/6-311+G(3df,2p)) model chemistries. G3 gives an average mean absolute deviation of 3.0 and 13.4 kJ/mol for the enthalpies and free energies, respectively, using the atomization method and 3.1 and 3.7 kJ/mol when bond separation reactions are employed. G3 and G3B3 are the most accurate overall; the related G3MP2 and G3MP2B3 are nearly as accurate and can compute larger molecules. CBS-QB3 was also found to be accurate but is more limited in the size of molecules that can be computed. The density functional energies were found to have large deviations from the literature values using either the atomization or the bond separation method. Regardless of the model employed, the free energies are increasingly underestimated by computation as the size of the molecule increases. A series of corrections applied to the aliphatic hydrocarbons is presented, which usually reduces the deviations to less than 4 kJ/mol regardless of the size of the molecule.