Using atomic clustering based on structural and electronic descriptors that consider surrounding environment to evaluate local properties of DFT functionals

We developed a method for evaluating the accuracies of the local properties of DFT functionals in detail using a clustering method based on machine learning and structural/electronic descriptors. We generated 36 clusters consistent with human intuition using 30,436 carbon atoms from the QM9 dataset. The results were used to evaluate 13C NMR chemical shifts calculated using 84 DFT functionals. Carbon atoms were grouped based on their similar environments, reducing errors within these groups. This enables more accurate assessment of the accuracy using a specific DFT functional. Therefore, the present atomic clustering provides more detailed insight into accuracy verification.

Influences of polarizability effect of alkyl group and homoring competition effect of substituents on the NMR spectra of salen-type Schiff base

Salen-type Schiff bases are a kind of important compounds and are widely used. In order to explore the effect of alkyl groups and substituents attached to aromatic ring on the chemical shifts, 63 title compounds were synthesized. Their ¹ H NMR and ¹³ C NMR spectra were obtained; and the effects of the alkyl chain length and substituents on the chemical shifts (δ_H (CHN), δ_C (CHN), δ_H (OH), and δ_C (COH)) were studied. The results show that (1) the alkyl polarizability effect index (PEI) has an important influence on the chemical shifts of the above four atoms, with the increase of PEI, the values of δ_H (CHN) and δc(CHN) decrease, and the values of δ_H (OH) and δ_C (COH) increase. (2) The influence of substituent X attached to aromatic ring on the chemical shift is related to its position by taking OH or CHN as reference. As for the effect of substituent on the chemical shifts, the effect of Hammett constant σ(X)_OH and excited-state substituent parameter σ CC ex X  OH with OH as reference are different from that ofσ(X)_CHN and σ CC ex X  CH  N with CHN as reference, and there is a "homoring competition effect" of the substituent. (3) The effect of the cross-interaction between X and OH on the chemical shift is also significantly different due to the different position of X. Quantitative correlation equations against chemical shifts were built for the four atoms, and the stability and prediction ability of the obtained equations were confirmed by leave-one-out cross validation.

Versatility of the Cyano Group in Intermolecular Interactions

Several cyano groups are added to an alkane, alkene, and alkyne group so as to construct a Lewis acid molecule with a positive region of electrostatic potential in the area adjoining these substituents. Although each individual cyano group produces only a weak π-hole, when two or more such groups are properly situated, they can pool their π-holes into one much more intense positive region that is located midway between them. A NH3 base is attracted to this site, where it forms a strong noncovalent bond to the Lewis acid, amounting to as much as 13.6 kcal/mol. The precise nature of the bonding varies a bit from one complex to the next but typically contains a tetrel bond to the C atoms of the cyano groups or the C atoms of the linkage connecting the C≡N substituents. The placement of the cyano groups on a cyclic system like cyclopropane or cyclobutane has a mild weakening effect upon the binding. Although F is comparable to C≡N in terms of electron-withdrawing power, the replacement of cyano by F substituents substantially weakens the binding with NH3.

Impact of intramolecular hydrogen bonding of gallic acid conformers on chemical shift through NMR spectroscopy

Intramolecular hydrogen bonding of gallic acid conformers was probed as a function of their dihedral angles using ¹³C nuclear magnetic resonance (NMR) chemical shift (δ_C). The quantum mechanically calculated ¹³C NMR chemical shift based on the most stable conformer (GA-I) in dimethylsulfoxide (DMSO) solution agrees to available measurement in the same solvent (RMSD = 0.95 ppm), better than to the measurement in solid phase (RMSD = 1.93 ppm). The accuracy of the calculated NMR chemical shift of the nominal but non-equivalent phenyl carbons C₍₃₎/C₍₇₎ and C₍₄₎/C₍₆₎ (ortho and meta to the acid -C₍₁₎OOH group) of GA may not be evaluated using the experimental measurements at room temperature. The splitting in chemical shift of the nominal phenyl carbons is able to be experimentally measured only in low temperature NMR and using quantum mechanical calculations. We further recognised that the C NMR chemical shifts of the nominal phenyl carbons (C₍₃₎/C₍₇₎ and C₍₄₎/C₍₆₎) encode information for intramolecular hydrogen bonding network formed by GA conformers. The ability to obtain accurate splitting of NMR chemical shifts for nominal carbons, therefore, determines the usefulness of the NMR technique as a probe for conformation of GA.

Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes

In this study, the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) method was applied for NMR chemical shift calculations of protein-ligand complexes. In the AF-QM/MM approach, the protein binding pocket is automatically divided into capped fragments (within ~200 atoms) for density functional theory (DFT) calculations of NMR chemical shifts. Meanwhile, the solvent effect was also included using the Poission-Boltzmann (PB) model, which properly accounts for the electrostatic polarization effect from the solvent for protein-ligand complexes. The NMR chemical shifts of neocarzinostatin (NCS)-chromophore binding complex calculated by AF-QM/MM accurately reproduce the large-sized system results. The 1H chemical shift perturbations (CSP) between apo-NCS and holo-NCS predicted by AF-QM/MM are also in excellent agreement with experimental results. Furthermore, the DFT calculated chemical shifts of the chromophore and residues in the NCS binding pocket can be utilized as molecular probes to identify the correct ligand binding conformation. By combining the CSP of the atoms in the binding pocket with the Glide scoring function, the new scoring function can accurately distinguish the native ligand pose from decoy structures. Therefore, the AF-QM/MM approach provides an accurate and efficient platform for protein-ligand binding structure prediction based on NMR derived information.

Theoretical study of the NMR chemical shift of Xe in supercritical condition

In this work we investigate the level of theory necessary for reproducing the non-linear variation of the ¹²⁹Xe nuclear magnetic resonance (NMR) chemical shift with the density of Xe in supercritical conditions. In detail we study how the ¹²⁹Xe chemical shift depends under supercritical conditions on electron correlation, relativistic and many-body effects. The latter are included using a sequential-QM/MM methodology, in which a classical MD simulation is performed first and the chemical shift is then obtained as an average of quantum calculations of 250 MD snapshots conformations carried out for Xe _n clusters (n = 2 - 8 depending on the density). The analysis of the relativistic effects is made at the level of 4-component Hartree-Fock calculations (4c-HF) and electron correlation effects are considered using second order Møller-Plesset perturbation theory (MP2). To simplify the calculations of the relativistic and electron correlation effects we adopted an additive scheme, where the calculations on the Xe _n clusters are carried out at the non-relativistic Hartree-Fock (HF) level, while electron correlation and relativistic corrections are added for all the pairs of Xe atoms in the clusters. Using this approach we obtain very good agreement with the experimental data, showing that the chemical shift of ¹²⁹Xe in supercritical conditions is very well described by cluster calculations at the HF level, with small contributions from relativistic and electron correlation effects.

The influence of Mg2+ coordination on 13C and 15N chemical shifts in CKI1RD protein domain from experiment and molecular dynamics/density functional theory calculations

Sequence dependence of (13) C and (15) N chemical shifts in the receiver domain of CKI1 protein from Arabidopsis thaliana, CKI1RD , and its complexed form, CKI1RD •Mg(2+), was studied by means of MD/DFT calculations. MD simulations of a 20-ns production run length were performed. Nine explicitly hydrated structures of increasing complexity were explored, up to a 40-amino-acid structure. The size of the model necessary depended on the type of nucleus, the type of amino acid and its sequence neighbors, other spatially close amino acids, and the orientation of amino acid NH groups and their surface/interior position. Using models covering a 10 and a 15 Å environment of Mg(2+), a semi-quantitative agreement has been obtained between experiment and theory for the V67-I73 sequence. The influence of Mg(2+) binding was described better by the 15 Å as compared to the 10 Å model. Thirteen chemical shifts were analyzed in terms of the effect of Mg(2+) insertion and geometry preparation. The effect of geometry was significant and opposite in sign to the effect of Mg(2+) binding. The strongest individual effects were found for (15) N of D70, S74, and V68, where the electrostatics dominated; for (13) Cβ of D69 and (15) N of K76, where the influences were equal, and for (13) Cα of F72 and (13) Cβ of K76, where the geometry adjustment dominated. A partial correlation between dominant geometry influence and torsion angle shifts upon the coordination has been observed.