Aqueous-Phase Conformations of Lactose, Maltose, and Sucrose and the Assessment of Low-Cost DFT Methods with the DSCONF Set of Conformers for the Three Disaccharides

Accurate Computation of Aqueous pKas 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

The use of static electronic structure calculations to compute solution-phase pKas 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 pKas 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 pKas 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 pKa 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 pKas 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.

Bond dissociation energies of ethyl valerate and tripropionin

CONTEXT

Due to the expected decrease in the availability of conventional oils, numerous studies are currently underway to find complementary sources of energy. Among the explored avenue is that of biofuels. Ethyl valerate (ETV) and tripropionin (TPP) are two biofuels whose thermal decomposition has not received the attention it deserves. Herein, we have evaluated the bond dissociation enthalpies (BDHs) to predict how easy it is to break some bonds in these compounds, and subsequently contribute to revealing the initiation step in their combustion reactions. Our computations consistently predict C4-C5 and C1-C2 bonds in ETV and TPP as the weakest bonds, likely to break first and initiate the thermal decomposition of these two compounds, respectively. The conformational changes in ETV and TPP have only a small influence on the BDHs of 1 kcal/mol at M06-2X/6-311 + G(3df,2p). B3LYP and ωB97XD appear to be the most affordable methods for estimating BDHs at 6-31G(d,p) as they give good results for ETV (RMSD: 2.94 kcal/mol and 3.22 kcal/mol) and performed better than CBS-QB3 (RMSD: 3.64 kcal/mol). Using a larger basis set, the M06-2X (RMSD: 3.61 kcal/mol) and ωB97XD (RMSD: 3.51 kcal/mol) functionals are found to provide the most accurate predictions at 6-311 + G(3df,2p) as compared to G4MP2.

METHODS

BDHs of ETV and TPP are computed using density functional theory (DFT) and quantum chemistry composite methods at 6-31G(d,p) and 6-311 + G(3df,2p) levels. Because of its reliability and accuracy in thermochemical calculations, the G4MP2 theory is used as a reference to gauge the performance of DFT methods. All the calculations were carried out using the Gaussian 09 program.

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

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.

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

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.

Searching for a Reliable Density Functional for Molecule-Environment Interactions, Found B97M-V/def2-mTZVP

In the present study, we have examined density functional theory methods for the calculation of the interaction energy between a small molecule and its environment. For simple systems such as a neutral solute in a neutral solvent, good accuracy can be attained using low-cost "3c" methods, in particular r²SCAN-3c. When part(s) of the system is charged, the accurate computation of the interactions is more challenging. In these cases, we find the B97M-V/def2-mTZVP method to agree well with reference values; it also shows good accuracy for the more straightforward neutral systems. Thus, B97M-V/def2-mTZVP provides a means for accurate and low-cost computation of interaction energies, notably the binding between a substrate or a drug molecule and an enzyme, which may facilitate rational drug design.

Small-Basis Set Density-Functional Theory Methods Corrected with Atom-Centered Potentials

Density functional theory (DFT) is currently the most popular method for modeling noncovalent interactions and thermochemistry. The accurate calculation of noncovalent interaction energies, reaction energies, and barrier heights requires choosing an appropriate functional and, typically, a relatively large basis set. Deficiencies of the density-functional approximation and the use of a limited basis set are the leading sources of error in the calculation of noncovalent and thermochemical properties in molecular systems. In this article, we present three new DFT methods based on the BLYP, M06-2X, and CAM-B3LYP functionals in combination with the 6-31G* basis set and corrected with atom-centered potentials (ACPs). ACPs are one-electron potentials that have the same form as effective-core potentials, except they do not replace any electrons. The ACPs developed in this work are used to generate energy corrections to the underlying DFT/basis-set method such that the errors in predicted chemical properties are minimized while maintaining the low computational cost of the parent methods. ACPs were developed for the elements H, B, C, N, O, F, Si, P, S, and Cl. The ACP parameters were determined using an extensive training set of 118655 data points, mostly of complete basis set coupled-cluster level quality. The target molecular properties for the ACP-corrected methods include noncovalent interaction energies, molecular conformational energies, reaction energies, barrier heights, and bond separation energies. The ACPs were tested first on the training set and then on a validation set of 42567 additional data points. We show that the ACP-corrected methods can predict the target molecular properties with accuracy close to complete basis set wavefunction theory methods, but at a computational cost of double-ζ DFT methods. This makes the new BLYP/6-31G*-ACP, M06-2X/6-31G*-ACP, and CAM-B3LYP/6-31G*-ACP methods uniquely suited to the calculation of noncovalent, thermochemical, and kinetic properties in large molecular systems.

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

We have examined the conformational space of model systems for the hydrogen-bonded and covalent linkages between the sugar and lignin components of lignocellulose. Specifically, glucose and paracoumaryl alcohol moieties are used in our models. Multistage screening protocols are used to identify and validate a set of lowest-energy isomers. We found a cost-effective screening process involving an initial screening with DFTB3/3ob using a 20 kJ mol^-1 threshold, a refinement with the SCANh/6-31+G(2d,p) method with a 10 kJ mol^-1 cutoff, a third step at the DSD-PBEP86/ma-def2-TZVP//MS1-D3/6-31+G(2d,p) level with the same 10 kJ mol^-1 threshold, and a last step at the CCSD(T)/CBS//B3LYP/cc-pVTZ level with a tighter 5 kJ mol^-1 threshold. The use of machine learning (with the London and Axilrod-Teller-Muto potential) can further accelerate the screening process. In general, all low-energy conformers are characterized by hydrogen bonding between the sugar and lignin moieties. We examined the interactions of covalently bonded sugar-lignin models with weak acids (HSO₃^-, H₂PO₃^-, HSeO₃^-, H₂citrate^-, etc.) and found that they interacted strongly with the oxygen of the sugar-O-lignin linkage. Our results suggest that acids such as dihydrogen citrate may be attractive alternatives to the commonly used HSO₃^- for lignocellulose processing.

Fast and Accurate Quantum Mechanical Modeling of Large Molecular Systems Using Small Basis Set Hartree-Fock Methods Corrected with Atom-Centered Potentials

There has been significant interest in developing fast and accurate quantum mechanical methods for modeling large molecular systems. In this work, by utilizing a machine learning regression technique, we have developed new low-cost quantum mechanical approaches to model large molecular systems. The developed approaches rely on using one-electron Gaussian-type functions called atom-centered potentials (ACPs) to correct for the basis set incompleteness and the lack of correlation effects in the underlying minimal or small basis set Hartree-Fock (HF) methods. In particular, ACPs are proposed for ten elements common in organic and bioorganic chemistry (H, B, C, N, O, F, Si, P, S, and Cl) and four different base methods: two minimal basis sets (MINIs and MINIX) plus a double-ζ basis set (6-31G*) in combination with dispersion-corrected HF (HF-D3/MINIs, HF-D3/MINIX, HF-D3/6-31G*) and the HF-3c method. The new ACPs are trained on a very large set (73 832 data points) of noncovalent properties (interaction and conformational energies) and validated additionally on a set of 32 048 data points. All reference data are of complete basis set coupled-cluster quality, mostly CCSD(T)/CBS. The proposed ACP-corrected methods are shown to give errors in the tenths of a kcal/mol range for noncovalent interaction energies and up to 2 kcal/mol for molecular conformational energies. More importantly, the average errors are similar in the training and validation sets, confirming the robustness and applicability of these methods outside the boundaries of the training set. In addition, the performance of the new ACP-corrected methods is similar to complete basis set density functional theory (DFT) but at a cost that is orders of magnitude lower, and the proposed ACPs can be used in any computational chemistry program that supports effective-core potentials without modification. It is also shown that ACPs improve the description of covalent and noncovalent bond geometries of the underlying methods and that the improvement brought about by the application of the ACPs is directly related to the number of atoms to which they are applied, allowing the treatment of systems containing some atoms for which ACPs are not available. Overall, the ACP-corrected methods proposed in this work constitute an alternative accurate, economical, and reliable quantum mechanical approach to describe the geometries, interaction energies, and conformational energies of systems with hundreds to thousands of atoms.

Accurate Thermochemistry for Main-Group Elements up to Xenon with the Wn-P34 Series of Composite Methods

In the present study, we introduce the accurate Wn-P34 quantum chemistry composite methods with applicability to heavy p-block elements up to xenon. For a set of thermochemical properties for prototypical third- and fourth-row species and for a diverse set of small light-main-group species, they show accuracies of ∼3 kJ mol^-1 or better. Overall, the Wn-P34 methods are comparable in accuracy to Wn, with a widened applicability to heavier elements. We have used Wn-P34 to compile the P34 set of accurate thermochemical values for heavy p-block species, and we have applied this set to assess a wide range of lower-cost methods. The results of our assessment show that the G4(MP2)-XK composite method provides adequate treatments for these species, but several widely used double-hybrid density functional theory (DH-DFT) methods show uncharacteristically large deviations. In contrast, we find it presently surprising that some pure and hybrid DFT methods such as TPSS and SCANh perform quite well. We hope that our findings and new tools would facilitate the application of computational chemistry for heavy elements, of which the properties are yet to be broadly explored.

Three-Dimensional Structures of Carbohydrates and Where to Find Them

Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.

Anion Binding Affinity: Acidity versus Conformational Effects

High-level quantum chemical calculations were used to elucidate the gas- and solution-phase conformational equilibria for a series of symmetrically substituted (thio)ureas, (thio)squaramides, and croconamides. Gas-phase calculations predict that the thermodynamic conformer of many of these anion receptors is not the dual-hydrogen-bond-facilitating anti-anti conformer as is commonly assumed. For N,N'-diaryl thiosquaramides and croconamides, the syn-syn conformer is typically the predominant conformer. Solution-phase calculations show that the anti-anti conformer is increasingly stabilized as the polarity of the solvent increases. However, the syn-syn conformer remains the lowest energy conformation for croconamides. These predictions are used to explain the acidity versus chloride binding affinity correlations recently reported for some of these compounds. The chloride binding constants for thioureas and croconamides are significantly lower than expected on the basis of their pK_a values, and this may be due in part to the need for these receptors to reorganize into the anti-anti conformer. Experimental NMR nuclear Overhauser effect (NOE) measurements of an asymmetrically substituted squaramide and its thio analogue are consistent with the syn-syn conformation being predominant at 298 K. The conformational equilibria should therefore be an important consideration for the design and development of future anion receptors and organocatalysts.