1,721,085 research outputs found
Free Energies of Hydration for Metal Ions from Heats of Vaporization
No full textConsistent
thermochemical data are of major importance for predicting
and rationalizing stability and reactivity throughout chemistry. The
free energy of hydration (ΔGhyd)
substantially defines the aqueous chemistry of metal ions and aids
our understanding of the properties of water and has thus been widely
studied both theoretically and experimentally. This paper first shows
that the experimental standard half reduction potential for the process
Mn+ + ne– → M is accurately described using a simplified version of
Trasatti’s thermochemical cycle involving the ionization potentials,
ΔGhyd of Mn+, and the standard heat of vaporization (ΔHvap) of M. This approximation, which neglects entropy,
is shown to be valid both by actual performance (uncertainty ∼0.1
V, R2 ∼ 0.99–1.00 for available
data for M3+ and M2+ ions) and by application
of Trouton’s rule for entropies of vaporization. Second, application
of the formula allows the identification of many ΔGhyd values not reported before. Together with previously
determined values, the compiled lists of ΔGhyd are the most complete so far reported and are all
thermochemically consistent; i.e., they agree with their corresponding
thermochemical cycles. The numbers use the convention ΔGhyd(H+) = −1100 kJ/mol and
SHE = +4.44 V but can be easily adjusted to other reference states
as appropriate. Some of the new ΔGhyd values established here are for the catalytically important d-transition
metal ions Rh3+, Re3+, Ir3+, Mo3+, W3+, Tc2+, Nb3+, Ta3+, Os3+, and Ru2+. Some, such as Ir3+, are among the most inert aqua ions known. The ΔGhyd values have an accuracy of ∼10 kJ/mol
and are recommended for use in thermochemical calculations, for interpretation
of the aqueous chemistry of the metal ions, and as benchmarks for
theoretical chemistry
Genotype-Property Patient-Phenotype Relations Suggest that Proteome Exhaustion Can Cause Amyotrophic Lateral Sclerosis
Get PDFLate-onset neurodegenerative diseases remain poorly understood as search continues for the perceived pathogenic protein species. Previously, variants in Superoxide Dismutase 1 (SOD1) causing Amyotrophic Lateral Sclerosis (ALS) were found to destabilize and reduce net charge, suggesting a pathogenic aggregation mechanism. This paper reports analysis of compiled patient data and experimental and computed protein properties for variants of human SOD1, a major risk factor of ALS. Both stability and reduced net charge correlate significantly with disease, with larger significance than previously observed. Using two independent methods and two data sets, a probability <3% (t-statistical test) is found that ALS-causing mutations share average stability with all possible 2907 SOD1 mutations. Most importantly, un-weighted patient survival times correlate strongly with the misfolded/unfolded protein copy number, expressed as an exponential function of the experimental stabilities (R-2 = 0.31, p = 0.002), and this phenotype is further aggravated by charge (R-2 = 0.51, p = 1.8 x 10-5). This finding suggests that disease relates to the copy number of misfolded proteins. Exhaustion of motor neurons due to expensive protein turnover of misfolded protein copies is consistent with the data but can further explain e. g. the expression-dependence of SOD1 pathogenicity, the lack of identification of a molecular toxic mode, elevated SOD1 mRNA levels in sporadic ALS, bioenergetic effects and increased resting energy expenditure in ALS patients, genetic risk factors affecting RNA metabolism, and recent findings that a SOD1 mutant becomes toxic when proteasome activity is recovered after washout of a proteasome inhibitor. Proteome exhaustion is also consistent with energy-producing mitochondria accumulating at the neuromuscular junctions where ALS often initiates. If true, this exhaustion mechanism implies a complete change of focus in treatment of ALS towards actively nursing the energy state and protein turnover of the motor neurons
A Quantitative Scale of Oxophilicity and Thiophilicity
No full textOxophilicity and thiophilicity are widely used concepts with no quantitative definition. In this paper, a simple, generic scale is developed that solves issues with reference states and system dependencies and captures empirically known tendencies toward oxygen. This enables a detailed analysis of the fundamental causes of oxophilicity. Notably, the notion that oxophilicity relates to Lewis acid hardness is invalid. Rather, oxophilicity correlates only modestly and inversely with absolute hardness and more strongly with electronegativity and effective nuclear charge. Since oxygen is highly electronegative, ionic bonding is stronger to metals of low electronegativity. Left-side d-block elements with low effective nuclear charges and electro-negativities are thus highly oxophilic, and the f-block elements, not because of their hardness, which is normal, but as a result of the small ionization energies of their outermost valence electrons, can easily transfer electrons to fulfill the electron demands of oxygen. Consistent with empirical experience, the most oxophilic elements are found in the left part of the d block, the lanthanides, and the actinides. The d-block elements differ substantially in oxophilicity, quantifying their different uses in a wide range of chemical reactions; thus, the use of mixed oxo- and thiophilic (i.e., "mesophilic") surfaces and catalysts as a design principle can explain the success of many recent applications. The proposed scale may therefore help to rationalize and improve chemical reactions more effectively than current qualitative considerations of oxophilicity
Halide Binding and Inhibition of Laccase Copper Clusters: The Role of Reorganization Energy
No full textLaccase-like proteins are multicopper oxidases involved in several biological and industrial processes. Their application is commonly limited due to inhibition by fluoride and chloride, and as-isolated proteins are often substantially activated by heat, suggesting that multiple redox states can complicate characterization. Understanding these processes at the molecular level is thus desirable but theoretically unexplored. This paper reports systematic calculations of geometries, reorganization energies, and ionization energies for all partly oxidized states of the trinuclear copper clusters in realistic models with similar to 200 atoms. Corrections for scalar-relativistic effects, dispersion, and thermal effects were estimated. Fluoride, chloride, hydroxide, or water was bound to the T2 copper site of the oxidized resting state, and the peroxo intermediate was also computed for reference. Antiferromagnetic coupling, assigned oxidation states, and general structures were consistent with known spectroscopic data. The computations show that (i) ligands bound to the T2 site substantially increase the reorganization energy of the second reduction of the resting state and reduce the redox potentials, providing a possible mechanism for inhibition; (ii) the reorganization energy is particularly large for F- but also high for Cl-, consistent with the experimental tendency of inhibition; (iii) reduction leads to release of Cl- from the T2 site, suggesting a mechanism for heat/reduction activation of laccases by dissociation of inhibiting halides or hydroxide from T2
Theoretical Study of Spin Crossover in 30 Iron Complexes
Get PDFSpin crossover was studied in 30 iron complexes using density functional theory to quantify the direction and magnitude of dispersion, relativistic effects, zero-point energies, and vibrational entropy. Remarkably consistent entropy−enthalpy compensation was identified. Zero-point energies favor high-spin by 9 kJ/mol on average; dispersion and relativistic effects both favor low-spin by 9 kJ/mol on average. These drivers dominate the thermodynamics (but not the transition nature) of SCO and should be considered in rational design of new spin crossover systems
Benchmarking Density Functionals for Chemical Bonds of Gold
Get PDFGold plays a major role in nanochemistry, catalysis, and electrochemistry. Accordingly, hundreds of studies apply density functionals to study chemical bonding with gold, yet there is no systematic attempt to assess the accuracy of these methods applied to gold. This paper reports a benchmark against 51 experimental bond enthalpies of AuX systems and seven additional polyatomic and cationic molecules. Twelve density functionals were tested, covering meta functionals, hybrids with variable HF exchange, double-hybrid, dispersion-corrected, and nonhybrid GGA functionals. The defined benchmark data set probes all types of bonding to gold from very electronegative halides that force Au+ electronic structure, via covalently bonded systems, hard and soft Lewis acids and bases that either work against or complement the softness of gold, the Au2 molecule probing gold's bond with itself, and weak bonds between gold and noble gases. Zero-point vibrational corrections are relatively small for Au-X bonds, ∼ 11-12 kJ/mol except for Au-H bonds. Dispersion typically provides ∼5 kJ/mol of the total bond enthalpy but grows with system size and is 10 kJ/mol for AuXe and AuKr. HF exchange and LYP correlation produce weaker bonds to gold. Most functionals provide similar trend accuracy, though somewhat lower for M06 and M06L, but very different numerical accuracy. Notably, PBE and TPSS functionals with dispersion display the smallest numerical errors and very small mean signed errors (0-6 kJ/mol), i.e. no bias toward over- or under-binding. Errors are evenly distributed versus atomic number, suggesting that relativistic effects are treated fairly; the mean absolute error is almost halved from B3LYP (45 kJ/mol) to TPSS and PBE (23 kJ/mol, including difficult cases); 23 kJ/mol is quite respectable considering the diverse bonds to gold and the complication of relativistic effects. Thus, studies that use DFT with effective core potentials for gold chemistry, with no alternative due to computational cost, are on solid ground using TPSS-D3 or PBE-D3
Co–C Dissociation of Adenosylcobalamin (Coenzyme B<sub>12</sub>): Role of Dispersion, Induction Effects, Solvent Polarity, and Relativistic and Thermal Corrections
No full textQuantum-chemical cluster modeling
is challenged in the limit of
large, soft systems by the effects of dispersion and solvent, and
well as other physical interactions. Adenosylcobalamin (AdoCbl,
coenzyme B12), as one of the most complex cofactors in
life, constitutes such a challenge. The cleavage of its unique organometallic
Co–C bond has inspired multiple studies of this cofactor. This
paper reports the fully relaxed potential energy surface of Co–C
cleavage of AdoCbl, including for the first time all side-chain interactions
with the dissociating Ado group. Various methods and corrections for
dispersion, relativistic effects, solvent polarity, basis set superposition
error, and thermal and vibrational effects were investigated, totaling
more than 550 single-point energies for the large model. The results
show immense variability depending on method, including solvation,
functional type, and dispersion, challenging the conceived accuracy
of methods used for such systems. In particular, B3LYP-D3 seems to
severely underestimate the Co–C bond strength, consistent with
previous results, and BP86 remains accurate for cobalamins when dispersion
interactions are accounted for
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
- …
