Modeling the Conformational Preference of the Lignocellulose Interface and Its Interaction with Weak Acids

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A recent study has examined the accuracy of NIST heats of formation for a set of C, H, and O-containing species with a proposed low-cost quantum chemistry approach. In the present study, we have used high-level methods such as W1X-2 to obtain these data more rigorously, which we have then used to assess the NIST and the previously computed values. We find that many of these NIST data that are as suggested to be unreliable by the previous study are indeed inconsistent with our high-level reference values. However, we also find substantial deviations for the previously computed values from our benchmark. Thus, we have assessed the performance of alternative low-cost methods. In our assessment, we have additionally examined C, H, N, and O-containing species for which heats of formation are available from the NIST database. We find the ωB97M-V/ma-def2-TZVP, DSD-PBEP86/ma-def2-TZVP, and CCSD(T)-F12b/aug′-cc-pVDZ methods to be adequate for obtaining heats of formation with the atomization approach, once their atomic energies are optimized with our benchmark. Notably, the low-cost ωB97M-V method yields values that agree to be within 10 kJ mol–1 for more than 90% of the (∼1500) species. A higher 20 kJ mol–1 threshold captures 98% of the data. The outlier species typically contain many electron-withdrawing (nitro) groups. In these cases, the use of isodesmic-type reactions rather than the atomization approach is more reliable. Our assessment has also identified significant outliers from the NIST database, for which experimental re-determination of the heats of formation would be desirable.

Section: Resultsmentioning

confidence: 99%

High-Level Quantum Chemistry Reference Heats of Formation for a Large Set of C, H, N, and O Species in the NIST Chemistry Webbook and the Identification and Validation of Reliable Protocols for Their Rapid Computation

Chan

2022

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“…In this regard, the focus has in the past been on main-group chemistry, in which studies are on-going. − In recent years, however, the scope has been expanded into other areas. They include statistical analysis of data sets, molecular transition-metal chemistry, transition-metal clusters, , heavy main-group species, , large biologically relevant systems, − and, in one of the latest studies, thermochemistry of NaCl clusters as a prototypical ionic compound …”

Section: Introductionmentioning

confidence: 99%

Compilation of Ionic Clusters with the Rock Salt Structure: Accurate Benchmark Thermochemical Data, Assessment of Quantum Chemistry Methods, and the Convergence Behavior of Lattice Energies

Chan

2023

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In the present study, computational quantum chemistry is used to obtain lattice energies (LEs) for a range of ionic clusters with the NaCl structure. Specifically, the compounds include NaF, NaCl, MgO, MgS, KF, CaO, and CaS clusters, (MX) n , with n = 1, 2, 4, 6, 8, 12, 16, 24, 32, 40, 50, 60, 75, 90, and 108. The highest-level W2 and W1X-2 methods are applied to the small clusters with n = 1 to 8 (the MX35 data set). The assessment with MX35 shows that, for the calculation of geometries and vibrational frequencies, the PBE0-D3(BJ) and PBE-D3(BJ) DFT methods are reasonable, but the calculation of atomization energies is more challenging. This is a result of different systematic deviations for clusters of different species. Thus, species-specific adjustments are applied for larger clusters, which are calculated with the DuT-D3 double-hybrid DFT method, the MN15 DFT method, and the PM7 semi-empirical method. They yield smoothly converging LEs to the bulk values. It is also found that, for the alkali-metal species, the LEs for a single molecule are ∼70% of the bulk values, while for the alkali-earth species, they are ∼80%. This has enabled a straightforward means to the first-principles estimation of LEs for similarly structured ionic compounds.

“…We also note that, for the use of single vs multiple conformers for the calculation of p K u , it is striking to know that we need just the lowest-energy one. However, this does not alleviate the need to find the lowest-energy conformer in the first place, and various low-cost conformational sampling protocols as has been employed by Chan in the recent years are anticipated to be useful and inexpensive alternate ways (as opposed to using DFT itself). , …”

Section: Resultsmentioning

confidence: 99%

“…However, this does not alleviate the need to find the lowest-energy conformer in the first place, and various low-cost conformational sampling protocols as has been employed by Chan in the recent years are anticipated to be useful and inexpensive alternate ways (as opposed to using DFT itself). 197,198 3.h.v. Improving the User Friendliness of pK-Yay.…”

Section: Hiv Extensions To Solvents Beyond Water/larger Systems and A...mentioning

confidence: 99%

Accurate Computation of Aqueous pK_as of Biologically Relevant Organic Acids: Overcoming the Challenges Posed by Multiple Conformers, Tautomeric Equilibria, and Disparate Functional Groups with the Fully Black-Box pK-Yay Method

Pereira,

Ramabhadran

2023

The use of static electronic structure calculations to compute solution-phase pK as offers a great advantage in that a macroscopic bulk property could be computed via microscopic computations involving very few molecules. There are various sources of errors in the quantum chemical calculations though. Overcoming these errors to accurately compute pK as of a plethora of acids is an active area of research in physical chemistry pursued by both computational as well as experimental chemists. We recently developed the pK-Yay method in our attempt to accurately compute aqueous pK as of strong and weak acids. The method is fully black-box, computationally inexpensive, and is very easy for even a nonexpert to use. However, the method was thus far tested on very few molecules (only 16 in all). Herein, in order to assess the future applicability of pK-Yay, we study the effect of multiple conformers, the presence of tautomers under equilibrium, and the impact of a wide variety of functional groups (derivatives of acetic acid with substituents at various positions, dicarboxylic acids, aromatic carboxylic acids, amines and amides, phenols and thiols, and fluorine bearing organic acids). Starting with more than 1000 conformers and tautomers, this study establishes that overall errors of ∼ 1.0 pK a units are routinely obtained for a majority of the molecules. Larger errors are noted in cases where multiple charges, intramolecular hydrogen bonding, and several ionizable functional groups are simultaneously present. An important conclusion to emerge from this work is that, the computed pK as are insensitive (difference <0.5) to whether we consider multiple conformers/tautomers or only choose the most stable conformer/tautomer. Further, pK-Yay captures the stereoelectronic effects arising due to differing axial vs equatorial pattern, and is useful to predict the dominant acid–base equilibrium in a system featuring several equilibria. Overall, pK-Yay may be employed in several chemical applications featuring organic molecules and biomonomers.