Influence of Density Functionals and Basis Sets on One-Bond Carbon-Carbon NMR Spin-Spin Coupling Constants

Development of 19 F-detected 1,1-ADEQUATE for the characterization of polyfluorinated and perfluorinated compounds

Polyfluorinated and perfluorinated compounds in the environment are a growing health concern. ¹⁹ F-detected variants of commonly employed heteronuclear shift correlation experiments such as heteronuclear single quantum correlation (HSQC) and heteronuclear multiple bond correlation (HMBC) are available; ¹⁹ F-detected experiments that employ carbon-carbon homonuclear coupling, in contrast, have never been reported. Herein, we report the measurement of the ¹ J_CC and ⁿ J_CC coupling constants of a simple perfluorinated phthalonitrile and the first demonstration of a ¹⁹ F-detected 1,1-ADEQUATE experiment.

Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations

Molecular dynamics (MD) simulation is widely used to complement ensemble-averaged experiments of intrinsically disordered proteins (IDPs). However, MD often suffers from limitations of inaccuracy. Here, we show that enhancing the sampling using Hamiltonian replica-exchange MD (HREMD) led to unbiased and accurate ensembles, reproducing small-angle scattering and NMR chemical shift experiments, for three IDPs of varying sequence properties using two recently optimized force fields, indicating the general applicability of HREMD for IDPs. We further demonstrate that, unlike HREMD, standard MD can reproduce experimental NMR chemical shifts, but not small-angle scattering data, suggesting chemical shifts are insufficient for testing the validity of IDP ensembles. Surprisingly, we reveal that despite differences in their sequence, the inter-chain statistics of all three IDPs are similar for short contour lengths (< 10 residues). The results suggest that the major hurdle of generating an accurate unbiased ensemble for IDPs has now been largely overcome.

Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation

Intrinsically disordered proteins (IDPs) are abundant in eukaryotic proteomes, play a major role in cell signaling, and are associated with human diseases. To understand IDP function it is critical to determine their configurational ensemble, i.e., the collection of 3-dimensional structures they adopt, and this remains an immense challenge in structural biology. Attempts to determine this ensemble computationally have been hitherto hampered by the necessity of reweighting molecular dynamics (MD) results or biasing simulation in order to match ensemble-averaged experimental observables, operations that reduce the precision of the generated model because different structural ensembles may yield the same experimental observable. Here, by employing enhanced sampling MD we reproduce the experimental small-angle neutron and X-ray scattering profiles and the NMR chemical shifts of the disordered N terminal (SH4UD) of c-Src kinase without reweighting or constraining the simulations. The unbiased simulation results reveal a weakly funneled and rugged free energy landscape of SH4UD, which gives rise to a heterogeneous ensemble of structures that cannot be described by simple polymer theory. SH4UD adopts transient helices, which are found away from known phosphorylation sites and could play a key role in the stabilization of structural regions necessary for phosphorylation. Our findings indicate that adequately sampled molecular simulations can be performed to provide accurate physical models of flexible biosystems, thus rationalizing their biological function.

Orthophosphate and Sulfate Utilization for C-E (E = P, S) Bond Formation via Trichlorosilyl Phosphide and Sulfide Anions

Reduction of phosphoric acid (H₃PO₄) or tetra- n-butylammonium bisulfate ([TBA][HSO₄]) with trichlorosilane leads to the formation of the bis(trichlorosilyl)phosphide ([P(SiCl₃)₂]^-, 1) and trichlorosilylsulfide ([Cl₃SiS]^-, 2) anions, respectively. Balanced equations for the formation of the TBA salts of anions 1 and 2 were formulated based on the identification of hexachlorodisiloxane and hydrogen gas as byproducts arising from these reductive processes: i) [H₂PO₄]^- + 10HSiCl₃ → 1 + 4O(SiCl₃)₂ + 6H₂ for P and ii) [HSO₄]^- + 9HSiCl₃ → 2 + 4O(SiCl₃)₂ + 5H₂ for S. Hydrogen gas was identified by its subsequent use to hydrogenate an alkene ((-)-terpinen-4-ol) using Crabtree's catalyst ([(COD)Ir(py)(PCy₃)][PF₆], COD = 1,5-cyclooctadiene, py = pyridine, Cy = cyclohexyl). Phosphide 1 was generated in situ by the reaction of phosphoric acid and trichlorosilane and used to convert an alkyl chloride (1-chlorooctane) to the corresponding primary phosphine, which was isolated in 41% yield. Anion 1 was also prepared from [TBA][H₂PO₄] and isolated in 62% yield on a gram scale. Treatment of [TBA]1 with an excess of benzyl chloride leads to the formation of tetrabenzylphosphonium chloride, which was isolated in 61% yield. Sulfide 2 was used as a thionation reagent, converting benzophenone to thiobenzophenone in 62% yield. It also converted benzyl bromide to benzyl mercaptan in 55% yield. The TBA salt of trimetaphosphate ([TBA]₃[P₃O₉]·2H₂O), also a precursor to anion 1, was found to react with either trichlorosilane or silicon(IV) chloride to provide bis(trimetaphosphate)silicate, [TBA]₂[Si(P₃O₉)₂], characterized by NMR spectroscopy, X-ray crystallography, and elemental analysis. Trichlorosilane reduction of [TBA]₂[Si(P₃O₉)₂] also provided anion 1. The electronic structures of 1 and 2 were investigated using a suite of theoretical methods; the computational studies suggest that the trichlorosilyl ligand is a good π-acceptor and forms σ-bonds with a high degree of s character.

Enhancing the utility of 1JCH coupling constants in structural studies through optimized DFT analysis

High accuracy for DFT-predicted ¹J_CH-couplings can be achieved without ad hoc corrections or empirical scaling by careful selection of the DFT method utilized for geometry optimization and J-coupling calculations.

Computational Prediction of 1 H and 13 C NMR Chemical Shifts for Protonated Alkylpyrroles: Electron Correlation and Not Solvation is the Salvation

Prediction of chemical shifts in organic cations is known to be a challenge. In this article we meet this challenge for α-protonated alkylpyrroles, a class of compounds not yet studied in this context, and present a combined experimental and theoretical study of the ¹³ C and ¹ H chemical shifts in three selected pyrroles. We have investigated the importance of the solvation model, basis set, and quantum chemical method with the goal of developing a simple computational protocol, which allows prediction of ¹³ C and ¹ H chemical shifts with sufficient accuracy for identifying such compounds in mixtures. We find that density functional theory with the B3LYP functional is not sufficient for reproducing all ¹³ C chemical shifts, whereas already the simplest correlated wave function model, Møller-Plesset perturbation theory (MP2), leads to almost perfect agreement with the experimental data. Treatment of solvent effects generally improves the agreement with experiment to some extent and can in most cases be accomplished by a simple polarizable continuum model. The only exception is the NH proton, which requires inclusion of explicit solvent molecules in the calculation.

Observation of untoward 3 Jcc correlations in 1,1-ADEQUATE spectra of pyrimidine analogs: Avoiding potential interpretation pitfalls

Recently, it has been reported that large ⁿ J_CC correlations can sometimes be observed in 1,1-ADEQUATE spectra with significant intensity, which opens the possibility of structural misassignment. In this work, we have focused on pyrimidine-based compounds, which exhibit multiple bond correlations in the 1,1-ADEQUATE experiment as a consequence of ³ J_CC coupling constants greater than 10 Hz. Results are supported by both the experimental measurement of ³ J_CC coupling constants in question using J-modulated-ADEQUATE and density functional theory calculations.

Carbon-carbon spin-spin coupling constants: Practical applications of theoretical calculations

Practical applications of theoretical calculations of carbon-carbon spin-spin coupling constants in particular classes of organic and bioorganic molecules are reviewed, concentrating mainly on saturated, unsaturated, aromatic and heteroaromatic compounds and their functional derivatives as well as on carbohydrates and natural compounds.

Evaluating the accuracy of theoretical one-bond 13 C─13 C scalar couplings and their ability to predict structure in a natural product

This study explores the feasibility of using a combination of experimental and theoretical 1-bond ¹³ C─¹³ C scalar couplings (¹ J_CC ) to establish structure in organic compounds, including unknowns. Historically, ⁿ J_CC and ⁿ J_CH studies have emphasized 2 and 3-bond couplings, yet ¹ J_CC couplings exhibit significantly larger variations. Moreover, recent improvements in experimental measurement and data processing methods have made ¹ J_CC data more available. Herein, an approach is evaluated in which a collection of theoretical structures is created from a partial nuclear magnetic resonance structural characterization. Computed ¹ J_CC values are compared to experimental data to identify candidates giving the best agreement. This process requires knowledge of the error in theoretical methods, thus the B3LYP, B3PW91, and PBE0 functionals are evaluated by comparing to 27 experimental values from INADEQUATE. Respective errors of ±1.2, ±3.8, and ±2.3 Hz are observed. An initial test of this methodology involves the natural product 5-methylmellein. In this case, only a single candidate matches experimental data with high statistical confidence. This analysis establishes the intramolecular hydrogen-bonding arrangement, ring heteroatom identity, and conformation at one position. This approach is then extended to hydroheptelidic acid, a natural product not fully characterized in prior studies. The experimental/theoretical approach proposed herein identifies a single best-fit structure from among 26 candidates and establishes, for the first time, 1 configuration and 3 conformations to complete the characterization. These results suggest that accurate and complete structural characterizations of many moderately sized organic structures (<800 Da) may be possible using only ¹ J_CC data.

Polar alicyclic rings: synthesis and structure of all cis-1,2,3,4-tetrafluorocyclopentane

All-cis-1,2,3,4-tetrafluorocyclopentane is synthesised and experiment and theory data reveal a very highly polar aliphatic with Janus like electropositive and electronegative faces.

Accurate Electron Densities at Nuclei Using Small Ramp-Gaussian Basis Sets

Electron densities at nuclei are difficult to calculate accurately with all-Gaussian basis sets because they lack an electron-nuclear cusp. The newly developed mixed ramp-Gaussian basis sets, such as R-31G, possess electron-nuclear cusps due to the presence of ramp functions in the basis. The R-31G basis set is a general-purpose mixed ramp-Gaussian basis set modeled on the 6-31G basis set. The prediction of electron densities at nuclei using R-31G basis sets for Li-F outperforms Dunning, Pople, and Jensen general purpose all-Gaussian basis sets of triple-ζ quality or lower and the cc-pVQZ basis set. It is of similar quality to the specialized pcJ-0 basis set which was developed with partial decontraction of core functions and extra high exponent s-Gaussians to predict electron density at the nucleus. These results show significant advantages in the properties of mixed ramp-Gaussian basis sets compared to all-Gaussian basis sets.

Understanding the conformational behaviour of Ac-Ala-NHMe in different media. A joint NMR and DFT study

The conformational behaviour of Ac-Ala-NHMe was studied in the gas-phase and in solution by theoretical calculations (B3LYP-D3/aug-cc-pVDZ level) and experimental (1)H NMR. The conformational preferences of this compound were shown to result from a complex interplay between the strengths of possible intramolecular hydrogen bonds, steric interactions, hyperconjugation, entropy effects and the overall dipole moments. The Ac-Ala-N(Me)2 derivative was studied in addition, to design a system akin to Ac-Ala-NHMe, but with disrupted intramolecular hydrogen bonds involving the -NHMe group, mimicking the effect of polar protic solvents.

Inter- and intramolecular CF···C=O interactions on aliphatic and cyclohexane carbonyl derivatives

Weak inter- and intra- molecular C(δ+)F(δ-)···C(δ+)=O(δ-) interactions were theoretically evaluated in 4 different sets of compounds at different theoretical levels. Intermolecular CH3F···C=O interactions were stabilizing by about 1 kcal mol(-1) for various carbonyl containing functional groups. Intramolecular CF···C=O interactions were also detected in aliphatic and fluorinated cyclohexane carbonyl derivatives. However, the stabilization provided by intramolecular CF···C=O interactions was not enough to govern the conformational preferences of compounds 2-4.

Conformational preferences of Ac-Gly-NHMe in solution

The conformational behaviour of Ac-Gly-NHMe and its fluorinated [CF₃-C(O)-Gly-NHMe] and N-methyl[Ac-Gly-N(Me)₂] derivatives is investigated in nonpolar, polar and polar protic solutions by NMR and IR spectroscopies and theoretical calculations.

Computational NMR coupling constants: shifting and scaling factors for evaluating 1JCH

Optimized shifting and/or scaling factors for calculating one-bond carbon-hydrogen spin-spin coupling constants have been determined for 35 combinations of representative functionals (PBE, B3LYP, B3P86, B97-2 and M06-L) and basis sets (TZVP, HIII-su3, EPR-III, aug-cc-pVTZ-J, ccJ-pVDZ, ccJ-pVTZ, ccJ-pVQZ, pcJ-2 and pcJ-3) using 68 organic molecular systems with 88 (1)JCH couplings including different types of hybridized carbon atoms. Density functional theory assessment for the determination of (1)JCH coupling constants is examined, comparing the computed and experimental values. The use of shifting constants for obtaining the calculated coupling improves substantially the results, and most models become qualitatively similar. Thus, for the whole set of couplings and for all approaches excluding those using the M06 functional, the root-mean-square deviations lie between 4.7 and 16.4 Hz and are reduced to 4-6.5 Hz when shifting constants are considered. Alternatively, when a specific rovibrational contribution of 5 Hz is subtracted from the experimental values, good results are obtained with PBE, B3P86 and B97-2 functionals in combination with HIII-su3, aug-cc-pVTZ-J and pcJ-2 basis sets.

Evaluation of Approximate Exchange-Correlation Functionals in Predicting One-Bond (31)P-(1)H NMR Indirect Spin-Spin Coupling Constants

This work benchmarks density functional theory, with several different exchange-correlation functionals, for prediction of isotropic one-bond phosphorus-hydrogen NMR spin-spin coupling constants (SSCCs). Our test set consists of experimental SSCCs from 30 diverse molecules representing multiple phosphorus bonding environments. The results suggest the importance of a balance between the choice of correlation functional and the admixture of nonlocal exchange. Overall, standard DFT methods appear to suffice for usefully accurate predictions of (31)P-(1)H SSCCs.

Measurement and applications of long-range heteronuclear scalar couplings: recent experimental and theoretical developments

The use of long-range heteronuclear couplings, in association with (1)H-(1)H scalar couplings and NOE restraints, has acquired growing importance for the determination of the relative stereochemistry, and structural and conformational information of organic and biological molecules. However, the routine use of such couplings is hindered by the inherent difficulties in their measurement. Prior to the advancement in experimental techniques, both long-range homo- and heteronuclear scalar couplings were not easily accessible, especially for very large molecules. The development of a large number of multidimensional NMR experimental methodologies has alleviated the complications associated with the measurement of couplings of smaller strengths. Subsequent application of these methods and the utilization of determined J-couplings for structure calculations have revolutionized this area of research. Problems in organic, inorganic and biophysical chemistry have also been solved by utilizing the short- and long-range heteronuclear couplings. In this minireview, we discuss the advantages and limitations of a number of experimental techniques reported in recent times for the measurement of long-range heteronuclear couplings and a few selected applications of such couplings. This includes the study of medium- to larger-sized molecules in a variety of applications, especially in the study of hydrogen bonding in biological systems. The utilization of these couplings in conjunction with theoretical calculations to arrive at conclusions on the hyperconjugation, configurational analysis and the effect of the electronegativity of the substituents is also discussed.

From CCSD(T)/aug-cc-pVTZ-J to CCSD(T) complete basis set limit isotropic nuclear magnetic shieldings via affordable DFT/CBS calculations

It is shown that a linear correlation exists between nuclear shielding constants for nine small inorganic and organic molecules (N(2), CO, CO(2), NH(3), CH(4), C(2)H(2), C(2)H(4), C(2)H(6) and C(6)H(6)) calculated with 47 methods (42 DFT methods, RHF, MP2, SOPPA, SOPPA(CCSD), CCSD(T)) and the aug-cc-pVTZ-J basis set and corresponding complete basis set results, estimated from calculations with the family of polarization-consistent pcS-n basis sets. This implies that the remaining basis set error of the aug-cc-pVTZ-J basis set is very similar in DFT and CCSD(T) calculations. As the aug-cc-pVTZ-J basis set is significantly smaller, CCSD(T)/aug-cc-pVTZ-J calculations allow in combination with affordable DFT/pcS-n complete basis set calculations the prediction of nuclear shieldings at the CCSD(T) level of nearly similar accuracy as those, obtained by fitting results obtained from computationally demanding pcS-n calculations at the CCSD(T) limit. A significant saving of computational efforts can thus be achieved by scaling inexpensive CCSD(T)/aug-cc-pVTZ-J calculations of nuclear isotropic shieldings with affordable DFT complete basis set limit corrections.

H2O, H2, HF, F2 and F2O nuclear magnetic shielding constants and indirect nuclear spin-spin coupling constants (SSCCs) in the BHandH/pcJ-n and BHandH/XZP Kohn-Sham limits

Good performance of segmented contracted basis sets XZP, where X = D, T, Q and 5, for obtaining H(2)O, H(2), HF, F(2) and F(2)O nuclear isotropic shielding constants in the BHandH Kohn-Sham basis set limit was shown. The results of two- and three-parameter complete basis set limit extrapolation schemes were compared with experimental results, earlier literature data and benchmark ab initio results. Similar convergence patterns of shieldings obtained from calculations using general purpose XZP basis sets and from polarization-consistent basis sets pcS-n and pcJ-n, where n = 0, 1, 2, 3 and 4, designed to accurately predict magnetic properties were observed. On the contrary, the SSCCs were more sensitive to the XZP basis set size and generally less accurate than those estimated using pcJ-n basis set family. The BHandH density functional markedly outperforms B3LYP method in predicting heavy atom shieldings and SSCCs values in the studied systems.

Prediction of water's isotropic nuclear shieldings and indirect nuclear spin-spin coupling constants (SSCCs) using correlation-consistent and polarization-consistent basis sets in the Kohn-Sham basis set limit

Density functional theory (DFT) was used to estimate water's isotropic nuclear shieldings and indirect nuclear spin-spin coupling constants (SSCCs) in the Kohn-Sham (KS) complete basis set (CBS) limit. Correlation-consistent cc-pVxZ and cc-pCVxZ (x = D, T, Q, 5, and 6), and their modified versions (ccJ-pVxZ, unc-ccJ-pVxZ, and aug-cc-pVTZ-J) and polarization-consistent pc-n and pcJ-n (n = 0, 1, 2, 3, and 4) basis sets were used, and the results fitted with a simple mathematical formula. The performance of over 20 studied density functionals was assessed from comparison with the experiment. The agreement between the CBS DFT-predicted isotropic shieldings, spin-spin values, and the experimental values was good and similar for the modified correlation-consistent and polarization-consistent basis sets. The BHandH method predicted the most accurate (1)H, (17)O isotropic shieldings and (1)J(OH) coupling constant (deviations from experiment of about -0.2 and -1 ppm and 0.6 Hz, respectively). The performance of BHandH for predicting water isotropic shieldings and (1)J(OH) is similar to the more advanced methods, second-order polarization propagator approximation (SOPPA) and SOPPA(CCSD), in the basis set limit.

A theoretical structural analysis of the factors that affect (1)J(NH), (1h)J(NH) and (2h)J(NN) in N-H...N hydrogen-bonded complexes

Calculations of (1)J(NH), (1h)J(NH) and (2h)J(NN) spin-spin coupling constants of 27 complexes presenting N-H...N hydrogen bonds have allowed to analyze these through hydrogen-bond coupling as a function of the hybridization of both nitrogen atoms and the charge (+1, 0, - 1) of the complex. The main conclusions are that the hybridization of N atom of the hydrogen bond donor is much more important than that of the hydrogen bond acceptor. Positive and negative charges (cationic and anionic complexes) exert opposite effects while the effect of the transition states 'proton-in-the-middle' is considerable.

Complete basis set B3LYP NMR calculations of CDCl3 solvent's water fine spectral details

The assignment of singlet at 1.55 ppm and the 1:1:1 triplet at 1.519 ppm to H(2)O and HOD in the 400 MHz (1)H NMR spectrum of CDCl(3) solvent were supported by complete basis set (CBS) GIAO-B3LYP calculated chemical shift and the CBS B3LYP estimated (2)J(D,H) spin-spin coupling constant (SSCC). The CBS fitting of B3LYP/cc-pCVxZ and B3LYP/pcJ-n predicted SSCC values, the accurate value of (2)J(D,H) = -1.082 +/- 0.030 Hz of HOD in chloroform-d(1) and the H/D isotopic shift of 0.0307(1) ppm were reported for the first time. The agreement between CBS B3LYP predicted chemical shift, spin-spin values and experiment was good.