NMR spectroscopy: quantum-chemical calculations

Low-Scaling, Efficient and Memory Optimized Computation of Nuclear Magnetic Resonance Shieldings within the Random Phase Approximation Using Cholesky-Decomposed Densities and an Attenuated Coulomb Metric

An efficient method for the computation of nuclear magnetic resonance (NMR) shielding tensors within the random phase approximation (RPA) is presented based on our recently introduced resolution-of-the-identity (RI) atomic orbital RPA NMR method [Drontschenko, V. J. Chem. Theory Comput. 2023, 19, 7542-7554] utilizing Cholesky decomposed density type matrices and employing an attenuated Coulomb RI metric. The introduced sparsity is efficiently exploited using sparse matrix algebra. This allows for an efficient and low-scaling computation of RPA NMR shielding tensors. Furthermore, we introduce a batching method for the computation of memory demanding intermediates that accounts for their sparsity. This extends the applicability of our method to even larger systems that would have been out of reach before, such as, e.g., a DNA strand with 260 atoms and 3408 atomic orbital basis functions.

Inhibition of DRP-1 mitochondrial mitophagy and fission by novel α-aminophosphonates bearing pyridine: synthesis, biological evaluations, and computer-aided design

Heterocyclic compounds play a crucial role in the drug discovery process and development due to their significant presence and importance. Here, we report a comprehensive analysis of α-aminophosphonates containing pyridine (3a-g), prepared according to a clear-cut, uncomplicated procedure. The phosphonates are thoroughly characterized using various methods, such as elemental analysis, mass spectrometry, proton and carbon NMR, and FT-IR. The molecular docking interactions between the phosphonate and DRP-1 target protein observed that compound 3d had the top-ranked binding energy towards DRP-1 with a value equal to - 9.54 kcal/mol and this theoretically proves its inhibitory efficacy against DRP-1 arbitrated mitochondrial fission. Besides, the anticancer characteristics of compound 3d showed the best IC50 against HepG-2, MCF-7, and Caco-2 which confirmed our results towards suppressing DRP-1 protein (in-silico), and it elucidated no cytotoxic effects against human normal cell line (WI-38). Further, its pharmacokinetics were observed theoretically using ADMET. Moreover,compound 3d investigated the most potent antimicrobial ability against two pathological fungal strains, A. flavus and C. albicans, and four bacterial strains, E. coli, B. subtillis, S. aureus, and P. aregeunosa. Additionally, compound 3d clarified a powerful antioxidant scavenging activity against DPPH and ABTS free radicals (in-vitro). Furthermore, Density functional theory (DFT) was used to study the molecular structures of the synthesized compounds 3a-g, utilizing 6-311++G(d,p) as the basis set and to learn more about the molecules' reactive sites, the energies of the molecular electrostatic potential (MEP), the lowest unoccupied molecular orbital (LUMO), and the highest occupied molecular orbital (HOMO) were observed. Theoretically, FT-IR and Nuclear magnetic resonance (NMR) measurements are calculated for every compound under investigation to show how theory and experiment relate. It was found that there was an excellent agreement between the theoretical and experimental data. Conclusively, all novel synthesized phosphonates could be used as pharmaceutical agents against pathogenic microbial strains and as anticancer candidates by inhibiting DRP-1-mediated mitochondrial mitophagy.

Electronic and Molecular Structures of a Series of Nickel Bis-1,1-Dithiolates

A series of homoleptic Ni bis-1,1-dithiolates, [Ni(S2C2RR')2]2- (R=CN, R'=CN, CO2Et, CONH2, Ph, Ph-4-Cl, Ph-4-OMe, Ph-4-NO2, Ph-3-CF3, Ph-4-CF3, Ph-4-CN; R=NO2, R'=H; R=R'=CO2Et) have been synthesized from the reaction of the alkali metal salt of the ligand and nickel chloride, and isolated as tetraphenylphosphonium or tetrabutylammonium salts. The complexes were characterized by X-ray crystallography, high-resolution mass spectrometry, and infrared (IR), nuclear magnetic resonance (NMR) and electronic absorption spectroscopies. The molecular structures show a rigidly square planar Ni(II) center linking two four-membered chelate rings whose dimensions are constant across the series. The electronic effect of the ligand substituent is revealed in the 13C NMR and electronic spectra, and corroborated by density functional calculations. Electron withdrawing groups deshield the low-field CS2 resonance, and the signature charge transfer band in the visible region is red-shifted. These observables have been accurately reproduced computationally, and revealed the Ni contribution to the ground state diminishes with decreasing electron withdrawing capacity of the ligand substituent. In contrast to 1,2-dithiolates, the redox inactivity afforded by 1,1-dithiolates stems from the smaller chelate ring and substantially reduced sulfur content that is key to stabilizing the radical form.

Spin-Spin Coupling Constant Based on Reference Interaction Site Model Self-Consistent Field with Constrained Spatial Electron Density

A method for computing spin-spin coupling constants (SSCCs) using the reference interaction site model self-consistent field with constrained spatial electron density (RISM-SCF-cSED) is proposed for the first time. Describing solvents using integral equation theory allows us to reflect solvent effects at atomic resolution in SSCCs while accounting for thermal fluctuations at a low computational cost. Applying the method to water, 1,1-difluoroethylene, and 1-methylaminomethylene-2-naphthalenone revealed that the solvent shift was evaluated to a greater extent than in the continuum solvent model. The origin of this phenomenon was analyzed in terms of the physical mechanisms underlying SSCCs.

Accurate Prediction of NMR Chemical Shifts: Integrating DFT Calculations with Three-Dimensional Graph Neural Networks

Computer prediction of NMR chemical shifts plays an increasingly important role in molecular structure assignment and elucidation for organic molecule studies. Density functional theory (DFT) and gauge-including atomic orbital (GIAO) have established a framework to predict NMR chemical shifts but often at a significant computational expense with a limited prediction accuracy. Recent advancements in deep learning methods, especially graph neural networks (GNNs), have shown promise in improving the accuracy of predicting experimental chemical shifts, either by using 2D molecular topological features or 3D conformational representation. This study presents a new 3D GNN model to predict 1H and 13C chemical shifts, CSTShift, that combines atomic features with DFT-calculated shielding tensor descriptors, capturing both isotropic and anisotropic shielding effects. Utilizing the NMRShiftDB2 data set and conducting DFT optimization and GIAO calculations at the B3LYP/6-31G(d) level, we prepared the NMRShiftDB2-DFT data set of high-quality 3D structures and shielding tensors with corresponding experimentally measured 1H and 13C chemical shifts. The developed CSTShift models achieve the state-of-the-art prediction performance on both the NMRShiftDB2-DFT test data set and external CHESHIRE data set. Further case studies on identifying correct structures from two groups of constitutional isomers show its capability for structure assignment and elucidation. The source code and data are accessible at https://yzhang.hpc.nyu.edu/IMA.

Analytical Second-Order Properties for the Random Phase Approximation: Nuclear Magnetic Resonance Shieldings

A method for the analytical computation of nuclear magnetic resonance (NMR) shieldings within the direct random phase approximation (RPA) is presented. As a starting point, we use the RPA ground-state energy expression within the resolution-of-the-identity approximation in the atomic-orbital formalism. As has been shown in a recent benchmark study using numerical second derivatives [Glasbrenner, M. J. Chem. Theory Comput. 2022, 18, 192], RPA based on a Hartree-Fock reference shows accuracies comparable to coupled cluster singles and doubles (CCSD) for NMR chemical shieldings. Together with the much lower computational cost of RPA, it has emerged as an accurate method for the computation of NMR shieldings. Therefore, we aim to extend the applicability of RPA NMR to larger systems by introducing analytical second-order derivatives, making it a viable method for the accurate and efficient computation of NMR chemical shieldings.

Evaluation of NMR predictors for accuracy and ability to reveal trends in 1 H NMR spectra of fatty acids

Four different nuclear magnetic resonance (NMR) predictors have been evaluated for their ability to predict 600-MHz ¹ H spectra of free fatty acids and fatty acid methyl esters of 20 common fatty acids. The predictors were evaluated on two main criteria: (1) their accuracy in direct prediction of the spectra (absolute accuracy) and (2) the ability to reveal trends or predict the change that occurs in the spectra as a result of a change in the fatty acid carbon chain, or by esterification of the free fatty acids to methyl esters (relative accuracy). The absolute accuracy in chemical shift prediction for fatty acids was good, compared with previous reports on a broader range of compounds. All four predictors had median prediction errors for chemical shifts of the signals in fatty acid methyl esters well below 0.1 ppm and as low as 0.015 ppm for one of the predictors. However, all predictors also had outliers with errors far above the upper interquartile range. In general, they also fail to reproduce trends of diagnostic value that were observed in the experimental data or properly predict the result of a minor change in molecular structure. All four predictors depend on experimental data from different origins. This may be a limiting factor for the relative accuracy of the predictors.

Importance of Noncovalent Interactions Involving Sulfur Atoms in Thiopeptide Antibiotics─Glycothiohexide α and Nocathiacin I

Noncovalent interactions involving sulfur atoms play essential roles in protein structure and function by significantly contributing to protein stability, folding, and biological activity. Sulfur is a highly polarizable atom that can participate in many types of noncovalent interactions including hydrogen bonding, sulfur-π interactions, and S-lone pair interactions, but the impact of these sulfur-based interactions on molecular recognition and drug design is still often underappreciated. Here, we examine, using quantum chemical calculations, the roles of sulfur-based noncovalent interactions in complex naturally occurring molecules representative of thiopeptide antibiotics: glycothiohexide α and its close structural analogue nocathiacin I. While donor-acceptor orbital interactions make only very small contributions, electrostatic and dispersion contributions are predicted to be significant in many cases. In pursuit of understanding the magnitudes and nature of these noncovalent interactions, we made potential structural modifications that could significantly expand the chemical space of effective thiopeptide antibiotics.

Solvent Dependent Nuclear Magnetic Resonance Molecular Parameters Based on a Polarization Consistent Screened Range Separated Hybrid Density Functional Theory Framework

Nuclear magnetic resonance (NMR) properties of solvated molecules are significantly affected by the solvent. We, therefore, employ a polarization consistent framework that efficiently addresses the solvent polarizing environment effects. Toward this goal a dielectric screened range separated hybrid (SRSH) functional is invoked with a polarizable continuum model (PCM) to properly represent the orbital gap in the condensed phase. We build on the success of range separated hybrid (RSH) functionals to address the erroneous tendency of traditional density functional theory (DFT) to collapse the orbital gap. Recently, the impact of RSH that properly opens up the orbital gap in gas-phase calculations on NMR properties has been assessed. Here, we report the use of SRSH-PCM that produces properly solute orbital gaps in calculating isotropic nuclear magnetic shielding and chemical shift parameters of molecular systems in the condensed phase. We show that in contrast to simpler DFT-PCM approaches, SRSH-PCM successfully follows expected dielectric constant trends.

Combined application of DP4+ and ANN-PRA to determine the relative configuration of natural products: The alpha-bisabol case study

The combination of computational methods and experimental data from Nuclear Magnetic Resonance (NMR) is a considerably valuable tool in the elucidation of new natural product structures and, also, in the structural revision of previously reported compounds. Until recently, only classical statistical parameters were used, for example, linear correlation coefficient (R² ), mean absolute error (MAE), or root mean square deviation (RMSD), as a way to statistically "validate" the structure pointed out by experimental NMR spectra. Regarding the resolution of the relative configuration of organic molecules, novel tools were available in the last few years to assist in the NMR elucidation process. The most relevant are DP4+, which is based on a Bayesian probability, and ANN-PRA, which is based on artificial neural networks. The combined application of these tools has become the most accurate and important alternative to solve structural and stereochemical problems in natural product chemistry. Therefore, herein, in this case study, we intended to promote these novel tools, exploring the strengths and limitations of each approach in resolving the relative configuration of the sesquiterpene alpha-bisabol. We also highlighted the advantages of the complementary use of H- and C-DP4+ to obtain optimal results in the differentiation of the stereoisomers, validating the proposal with ANN-PRA method.

Electronic and Optical Properties of Eu2+-Activated Narrow-Band Phosphors for Phosphor-Converted Light-Emitting Diode Applications: Insights from a Theoretical Spectroscopy Perspective

In this work, we present a computational protocol that is able to predict the experimental absorption and emission spectral shapes of Eu²⁺-doped phosphors. The protocol is based on time-dependent density functional theory and operates in conjunction with an excited-state dynamics approach. It is demonstrated that across the study set consisting of representative examples of nitride, oxo-nitride, and oxide Eu²⁺-doped phosphors, the energy distribution and the band shape of the emission spectrum are related to the nature of the 4f–5d transitions that are probed in the absorption process. Since the 4f orbitals are very nearly nonbonding, the decisive quantity is the covalency of the 5d acceptor orbitals that become populated in the electronically excited state that leads to emission. The stronger the (anti) bonding interaction between the lanthanide and the ligands is in the excited state, the larger will be the excited state distortion. Consequently, the corresponding emission will get broader due to the vibronic progression that is induced by the structural distortion. In addition, the energy separation of the absorption bands that are dominated by states with valence 4f–5d and a metal to ligand charge transfer character defines a measure for the thermal quenching of the studied Eu²⁺-doped phosphors. Based on this analysis, simple descriptors are identified that show a strong correlation with the energy position and bandwidth of the experimental emission bands without the need for elaborate calculations. Overall, we believe that this study serves as an important reference for designing new Eu²⁺-doped phosphors with desired photoluminescence properties.

Revisiting the structure of Heliannuol L: A computational approach

Recently, structural elucidation of natural products has undergone a revolution. The combined use of different modern spectroscopic methods has allowed obtaining a complete structural assignment of natural products using small amounts of sample. However, despite the extraordinary ongoing advances in spectroscopy, the mischaracterization of natural products has been and remains a recurrent problem, especially when the substance presents several stereogenic centers. The misinterpretation of nuclear magnetic resonance (NMR) data has resulted in frequent reports addressing structural reassignment. In this context, a great effort has been devoted to developing quantum chemical calculations that simulate NMR parameters accurately, allowing to achieve a more precise spectral interpretation. In this work, we employed a protocol for theoretical calculations of ¹ H NMR chemical shifts and coupling constants using density functional theory (DFT), followed by the application of the DP4+ method to revisit the structure of Heliannuol L, a member of the Heliannuol class, isolated from Helianthus annuus. Our results indicate that the originally proposed structure of Heliannuol L needs a stereochemical reassignment, placing the hydroxyl bonded to C10 in the opposite side of the methyl and hydroxyl groups bonded to C7 and C8, respectively.

Computational NMR of charged systems

This review covers NMR computational aspects of charged systems-carbocations, heterocations, and heteroanions, which were extensively studied in a number of laboratories worldwide, first of all, at the Loker Hydrocarbon Research Institute in California directed for several decades by a distinguished scientist, the Nobel laureate George Andrew Olah. The first part of the review briefly outlines computational background of the modern theoretical methods applied to the calculation of chemical shifts and spin-spin coupling constants at the DFT and the non-empirical levels. The second part of the review deals with the historical results, advances, and perspectives of the computational NMR of classical carbocations like methyl cation, CH₃⁺ , and protonated methane, CH₅⁺ , together with their numerous homologs and derivatives. The third and the forth parts of this survey are focused on the NMR computational aspects of accordingly, heterocations and heteroanions, the organic and inorganic ions with a charge localized mainly on heteroatoms like boron, oxygen, nitrogen, and heavier elements.

Extended Benchmark Set of Main-Group Nuclear Shielding Constants and NMR Chemical Shifts and Its Use to Evaluate Modern DFT Methods

An extended theoretical benchmark set, NS372, for light main-group nuclear shieldings and NMR shifts has been constructed based on high-level GIAO-CCSD(T)/pcSseg-3//CCSD(T)/cc-pVQZ reference data. After removal of the large static-correlation cases O₃, F₃^-, and BH from the statistical evaluations for the ¹⁷O, ¹⁹F, and ¹¹B subsets, the benchmark comprises overall 372 shielding values in 117 molecules with a wide range of electronic-structure situations, containing 124 ¹H, 14 ¹¹B, 93 ¹³C, 43 ¹⁵N, 31 ¹⁷O, 47 ¹⁹F, 14 ³¹P, and 6 ³³S shielding constants. The CCSD(T)/pcSseg-3 data are shown to be close to the basis-set and method limit and thus provide an excellent benchmark to evaluate more approximate methods, such as density functional approaches. This dataset has been used to evaluate Hartree-Fock (HF) and MP2, and a wide range of exchange-correlation functionals from local density approximation (LDA) to generalized gradient approximations (GGAs) and meta-GGAs (focusing on their current-density functional implementations), as well as global hybrid, range-separated hybrid, local hybrid, and double-hybrid functionals. Starting with absolute shielding constants, the DSD-PBEP86 double hybrid is confirmed to provide the highest accuracy, with an aggregate relative mean absolute error (rel. MAE) of only 0.9%, followed by MP2 (1.1%). MP2 and double hybrids only show larger errors for a few systems with the largest static-correlation effects. The double-hybrid B2GP-PLYP, the two local hybrids cLH12ct-SsirPW92 and cLH12ct-SsifPW92, and the current-density functional meta-GGA cB97M-V follow closely behind (all 1.5%), as do some further functionals, cLH20t and cMN15-L (both 1.6%), as well as B2PLYP and KT3 (both 2.0%). Functionals on the lower rungs of the usual ladder offer the advantage of lower computational cost and access to larger molecules. Closer examination also reveals the best-performing methods for individual nuclei in the test set. Different ways of treating τ-dependent functionals are evaluated. When moving from absolute shielding constants to chemical shifts, some of the methods can benefit from systematic error compensation, and the overall error range somewhat narrows. Further methods now achieve the 2% threshold of relative MAEs, including functionals based on TPSS (TPSSh, cmPSTS).

Molecular search by NMR spectrum based on evaluation of matching between spectrum and molecule

Inferring molecular structures from experimentally measured nuclear magnetic resonance (NMR) spectra is an important task in many chemistry applications. Herein, we present a novel method implementing an automated molecular search by NMR spectrum. Given a query spectrum and a pool of candidate molecules, the matching score of each candidate molecule with respect to the query spectrum is evaluated by introducing a molecule-to-spectrum estimation procedure. The candidate molecule with the highest matching score is selected. This procedure does not require any prior knowledge of the corresponding molecular structure nor laborious manual efforts by chemists. We demonstrate the effectiveness of the proposed method on molecular search using ¹³C NMR spectra.

Computational NMR of Carbohydrates: Theoretical Background, Applications, and Perspectives

This review is written amid a marked progress in the calculation of NMR parameters of carbohydrates substantiated by a vast amount of experimental data coming from several laboratories worldwide. By no means are we trying to cover in the present compilation a huge amount of all available data. The main idea of the present review was only to outline general trends and perspectives in this dynamically developing area on the background of a marked progress in theoretical and computational NMR. Presented material is arranged in three basic sections: (1)-a brief theoretical introduction; (2)-applications and perspectives in computational NMR of monosaccharides; and (3)-calculation of NMR chemical shifts and spin-spin coupling constants of di- and polysaccharides.

Automated fragmentation quantum mechanical calculation of 13C and 1H chemical shifts in molecular crystals

In this work, the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach was applied to calculate the ¹³C and ¹H nuclear magnetic resonance (NMR) chemical shifts in molecular crystals. Two benchmark sets of molecular crystals were selected to calculate the NMR chemical shifts. Systematic investigation was conducted to examine the convergence of AF-QM/MM calculations and the impact of various density functionals with different basis sets on the NMR chemical shift prediction. The result demonstrates that the calculated NMR chemical shifts are close to convergence when the distance threshold for the QM region is larger than 3.5 Å. For ¹³C chemical shift calculations, the mPW1PW91 functional is the best density functional among the functionals chosen in this study (namely, B3LYP, B3PW91, M06-2X, M06-L, mPW1PW91, OB98, and OPBE), while the OB98 functional is more suitable for the ¹H NMR chemical shift prediction of molecular crystals. Moreover, with the B3LYP functional, at least a triple-ζ basis set should be utilized to accurately reproduce the experimental ¹³C and ¹H chemical shifts. The employment of diffuse basis functions will further improve the accuracy for ¹³C chemical shift calculations, but not for the ¹H chemical shift prediction. We further proposed a fragmentation scheme of dividing the central molecule into smaller fragments. By comparing with the results of the fragmentation scheme using the entire central molecule as the core region, the AF-QM/MM calculations with the fragmented central molecule can not only achieve accurate results but also reduce the computational cost. Therefore, the AF-QM/MM approach is capable of predicting the ¹³C and ¹H NMR chemical shifts for molecular crystals accurately and effectively, and could be utilized for dealing with more complex periodic systems such as macromolecular polymers and biomacromolecules. The AF-QM/MM program for molecular crystals is available at https://github.com/shiman1995/NMR.

Computation of NMR Shielding Constants for Solids Using an Embedded Cluster Approach with DFT, Double-Hybrid DFT, and MP2

In this work, we explore the accuracy of post-Hartree–Fock (HF) methods and double-hybrid density functional theory (DFT) for the computation of solid-state NMR chemical shifts. We apply an embedded cluster approach and investigate the convergence with cluster size and embedding for a series of inorganic solids with long-range electrostatic interactions. In a systematic study, we discuss the cluster design, the embedding procedure, and basis set convergence using gauge-including atomic orbital (GIAO) NMR calculations at the DFT and MP2 levels of theory. We demonstrate that the accuracy obtained for the prediction of NMR chemical shifts, which can be achieved for molecular systems, can be carried over to solid systems. An appropriate embedded cluster approach allows one to apply methods beyond standard DFT even for systems for which long-range electrostatic effects are important. We find that an embedded cluster should include at least one sphere of explicit neighbors around the nuclei of interest, given that a sufficiently large point charge and boundary effective potential embedding is applied. Using the pcSseg-3 basis set and GIAOs for the computation of nuclear shielding constants, accuracies of 1.6 ppm for ⁷Li, 1.5 ppm for ²³Na, and 5.1 ppm for ³⁹K as well as 9.3 ppm for ¹⁹F, 6.5 ppm for ³⁵Cl, 7.4 ppm for ⁷⁹Br, and 7.5 ppm for ²⁵Mg as well as 3.8 ppm for ⁶⁷Zn can be achieved with MP2. Comparing various DFT functionals with HF and MP2, we report the superior quality of results for methods that include post-HF correlation like MP2 and double-hybrid DFT.

Recent advances in computational 31 P NMR: Part 1. Chemical shifts

This is the first part of two closely related reviews dealing with the computation of phosphorus-31 nuclear magnetic resonance chemical shifts in a wide series of organophosphorus compounds including complexes, clusters, and bioorganic phosphorus compounds. In particular, the analysis of the accuracy factors, such as substitution effects, solvent effects, vibrational corrections, and relativistic effects, is presented. This review is dedicated to the Full Member of the Russian Academy of Sciences Professor Boris A. Trofimov in view of his invaluable contribution to the field of synthesis, nuclear magnetic resonance, and computation studies of organophosphorus compounds.

Recent advances in computational 31 P NMR: Part 2. Spin-spin coupling constants

This is the second part of two closely related reviews dealing with the computation of ³¹ P nuclear magnetic resonance (NMR) parameters in a wide range of phosphorous containing compounds. The first part of this review concentrated primarily on the computation of ³¹ P NMR chemical shifts, whereas the second part concerns the calculation of spin-spin coupling constants involving phosphorus nucleus, focusing primarily on their stereochemical dependencies and stereodynamic behavior in particular classes of organophosphorus compounds. This review is dedicated to the Full Member of the Russian Academy of Sciences Professor Boris A. Trofimov in view of his invaluable contribution to the field of synthesis, NMR, and computation studies of organophosphorus compounds.

NMR crystallography of molecular organics

Developments of NMR methodology to characterise the structures of molecular organic structures are reviewed, concentrating on the previous decade of research in which density functional theory-based calculations of NMR parameters in periodic solids have become widespread. With a focus on demonstrating the new structural insights provided, it is shown how "NMR crystallography" has been used in a spectrum of applications from resolving ambiguities in diffraction-derived structures (such as hydrogen atom positioning) to deriving complete structures in the absence of diffraction data. As well as comprehensively reviewing applications, the different aspects of the experimental and computational techniques used in NMR crystallography are surveyed. NMR crystallography is seen to be a rapidly maturing subject area that is increasingly appreciated by the wider crystallographic community.

Computational 1 H NMR: Part 1. Theoretical background

This is the first one of the three closely interrelated reviews to be published in Magnetic Resonance in Chemistry dealing with accordingly theoretical background, chemical applications, and biochemical studies of and by means of computational ¹ H NMR. Presented in the first part of the review is a general outline of the modern theoretical methods and accuracy factors of computational ¹ H NMR involving locally dense basis set schemes, solvent effects, vibrational corrections, and relativistic effects performed at the density functional theory and/or nonempirical levels. This review is dedicated to Prof. Stephan Sauer in view of his invaluable contribution to the field of computational nuclear magnetic resonance.

Effect of linewidth on estimation of metabolic concentration when using water lineshape spectral model fitting for single voxel proton spectroscopy at 7 T

Good B₀ field homogeneity is considered an essential requirement to obtain high-quality MRS data. Many commonly used spectral fitting methods assume that all metabolite signals have Lorentzian or Gaussian shapes. However, B₀ inhomogeneity can both broaden the linewidth and modify the lineshape. In this study, it is hypothesized that a realistic metabolite fitting model, which accounts for B₀ homogeneity on the basis of the water lineshape, will improve the accuracy of estimation of metabolite concentrations. In-vivo water suppressed/unsuppressed single voxel spectroscopy signals were acquired under three different B₀ field homogeneity regimes. Individual realistic basis sets were created for each acquisition. Frequency-domain spectral fitting with LCModel was used to quantify the metabolite concentrations with fitting uncertainties given in terms of the Cramer-Rao lower bound. The quantification results obtained using the water lineshape basis set yielded similar concentrations independent of linewidth and showed a larger fitting error as the linewidth increased. The conventional approach, however quantifies metabolite concentrations with greater variations despite showing a supposedly improved fitting quality. The water lineshape basis set achieved single voxel spectroscopy accuracy that is less sensitive to the linewidth compared to the conventional spectral fitting method for the range of linewidths used in this study, but the precision deteriorated with worsening B₀ field inhomogeneity. The beneficial effect was ascribed to a reduction in the number of degrees of freedom when using the water lineshape to generate the basis set.

Computational protocols for calculating 13C NMR chemical shifts

The most recent results dealing with the computation of ¹³C NMR chemical shifts in chemistry (small molecules, saturated, unsaturated and aromatic compounds, heterocycles, functional derivatives, coordination complexes, carbocations, and natural products) are reviewed, paying special attention to theoretical background and accuracy, the latter involving solvent effects, vibrational corrections, and relativistic effects.

Recent trends in the structural revision of natural products

Covering: 2012 to 2017 This article reviews recent reports on the structural revision of natural products. Through a critical assessment of the original and revised published structures, the article addresses why each structure was targeted for revision, discusses the techniques and key discrepancies that led to the proposal of the revised structure, and offers measures that may have been taken during the original structure determination to prevent error. With the revised structures in hand, weaknesses of original proposals are assessed, providing a better understanding on the logic behind structure determination.

A full additive QM/MM scheme for the computation of molecular crystals with extension to many-body expansions

An additive quantum mechanics/molecular mechanics (QM/MM) model for the theoretical investigation of molecular crystals (AC-QM/MM) is presented. At the one-body level, a single molecule is chosen as the QM region. The MM region around it consists of a finite cluster of explicit MM atoms, represented by point charges and Lennard-Jones potentials, with additional background charges to mimic periodic electrostatics. Cluster charges are QM-derived and calculated self-consistently to ensure a polarizable embedding. We have also considered the extension to many-body QM corrections, calculating the interactions of a central molecule to neighboring units in the crystal. Full gradient expressions have been derived, also including symmetry information. The scheme allows for the calculation of molecular properties as well as unconstrained optimizations of the molecular geometry and cell parameters with respect to the lattice energy. Benchmarking the approach with the X23 reference set confirms the convergence pattern of the many-body extension although a comparison to plane-wave density functional theory reveals a systematic overestimation of cohesive energies by 6-16 kJ mol^-1. While the scheme primarily aims to provide an inexpensive and flexible way to model a molecule in a crystal environment, it can also be used to reach highly accurate cohesive energies by the straightforward application of wave function correlated approaches. Calculations with local coupled cluster with singles, doubles, and perturbative triples, albeit limited to numerical gradients, show an impressive agreement with experimental estimates for small molecular crystals.

Theoretical calculations of carbon-hydrogen spin-spin coupling constants

Structural applications of theoretical calculations of carbon-hydrogen spin-spin coupling constants are reviewed covering papers published mainly during the last 10-15 years with a special emphasis on the most notable studies of hybridization, substitution and stereoelectronic effects together with the investigation of hydrogen bonding and intermolecular interactions. The wide scope of different applications of calculated carbon-hydrogen couplings in the structural elucidation of particular classes of organic and bioorganic molecules is reviewed, concentrating mainly on saturated, unsaturated, aromatic and heteroaromatic compounds and their functional derivatives, as well as on natural compounds and carbohydrates. The review is dedicated to Professor Emeritus Michael Barfield in view of his invaluable pioneering contribution to this field.

Fully Automated Quantum-Chemistry-Based Computation of Spin-Spin-Coupled Nuclear Magnetic Resonance Spectra

We present a composite procedure for the quantum‐chemical computation of spin–spin‐coupled ¹H NMR spectra for general, flexible molecules in solution that is based on four main steps, namely conformer/rotamer ensemble (CRE) generation by the fast tight‐binding method GFN‐xTB and a newly developed search algorithm, computation of the relative free energies and NMR parameters, and solving the spin Hamiltonian. In this way the NMR‐specific nuclear permutation problem is solved, and the correct spin symmetries are obtained. Energies, shielding constants, and spin–spin couplings are computed at state‐of‐the‐art DFT levels with continuum solvation. A few (in)organic and transition‐metal complexes are presented, and very good, unprecedented agreement between the theoretical and experimental spectra was achieved. The approach is routinely applicable to systems with up to 100–150 atoms and may open new avenues for the detailed (conformational) structure elucidation of, for example, natural products or drug molecules.

Pharmaceutical cocrystals, salts and polymorphs: Advanced characterization techniques

The main goal of a novel drug development is to obtain it with optimal physiochemical, pharmaceutical and biological properties. Pharmaceutical companies and scientists modify active pharmaceutical ingredients (APIs), which often are cocrystals, salts or carefully selected polymorphs, to improve the properties of a parent drug. To find the best form of a drug, various advanced characterization methods should be used. In this review, we have described such analytical methods, dedicated to solid drug forms. Thus, diffraction, spectroscopic, thermal and also pharmaceutical characterization methods are discussed. They all are necessary to study a solid API in its intrinsic complexity from bulk down to the molecular level, gain information on its structure, properties, purity and possible transformations, and make the characterization efficient, comprehensive and complete. Furthermore, these methods can be used to monitor and investigate physical processes, involved in the drug development, in situ and in real time. The main aim of this paper is to gather information on the current advancements in the analytical methods and highlight their pharmaceutical relevance.

Association of symmetrical alkane diols with pyridine: DFT/GIAO calculation of 1 H NMR chemical shifts

Proton nuclear magnetic resonance (NMR) shifts of the free diol and of its 1 : 1 and 1 : 2 hydrogen-bonded complexes with pyridine have been computed for five symmetrical alkane diols on the basis of density functional theory, by applying the gauge-including atomic orbital method to geometry-optimized conformers. For certain conformers, intramolecular OH···OH interactions, evidenced by high NMR OH proton shifts, are further enhanced on going from the free diol to the corresponding 1 : 1 diol/pyridine complex. This is confirmed by atoms-in-molecules and non-covalent interaction plots. The computed OH and CH proton shifts for the diol and the two complexes correlate well with values obtained by analysing data from the NMR titration of the diols in benzene against pyridine. Shift values for the diols in neat pyridine are calculated by weighting the shifts of the various protons in the three forms (free diol, 1 : 1 and 1 : 2 diol/pyridine complexes) according to the experimentally determined association constants. The results are in good agreement with those observed, and after empirical scaling, the root mean square difference is 0.18 ppm. Copyright © 2016 John Wiley & Sons, Ltd.

Modeling Polymorphic Molecular Crystals with Electronic Structure Theory

Interest in molecular crystals has grown thanks to their relevance to pharmaceuticals, organic semiconductor materials, foods, and many other applications. Electronic structure methods have become an increasingly important tool for modeling molecular crystals and polymorphism. This article reviews electronic structure techniques used to model molecular crystals, including periodic density functional theory, periodic second-order Møller-Plesset perturbation theory, fragment-based electronic structure methods, and diffusion Monte Carlo. It also discusses the use of these models for predicting a variety of crystal properties that are relevant to the study of polymorphism, including lattice energies, structures, crystal structure prediction, polymorphism, phase diagrams, vibrational spectroscopies, and nuclear magnetic resonance spectroscopy. Finally, tools for analyzing crystal structures and intermolecular interactions are briefly discussed.

(1)H NMR spectra of alcohols in hydrogen bonding solvents: DFT/GIAO calculations of chemical shifts

Proton nuclear magnetic resonance (NMR) shifts of aliphatic alcohols in hydrogen bonding solvents have been computed on the basis of density functional theory by applying the gauge-including atomic orbital method to geometry-optimized alcohol/solvent complexes. The OH proton shifts and hydrogen bond distances for methanol or ethanol complexed with pyridine depend very much on the functional employed and very little on the basis set, provided it is sufficiently large to give the correct quasi-linear hydrogen bond geometry. The CH proton shifts are insensitive to both the functional and the basis set. NMR shifts for all protons in several alcohol/pyridine complexes are calculated at the Perdew, Burke and Ernzerhof PBE0/cc-pVTZ//PBE0/6-311 + G(d,p) level in the gas phase. The results correlate with the shifts for the pyridine-complexed alcohols, determined by analysing data from the NMR titration of alcohols against pyridine. More pragmatically, computed shifts for a wider range of alcohols correlate with experimental shifts in neat pyridine. Shifts for alcohols in dimethylsulfoxide, based on the corresponding complexes in the gas phase, correlate well with the experimental values, but the overall root mean square difference is high (0.23 ppm), shifts for the OH, CHOH and other CH protons being systematically overestimated, by averages of 0.42, 0.21 and 0.06 ppm, respectively. If the computed shifts are corrected accordingly, a very good correlation is obtained with a gradient of 1.00 ± 0.01, an intercept of 0.00 ± 0.02 ppm and a root mean square difference of 0.09 ppm. This is a modest improvement on the result of applying the CHARGE programme to a slightly different set of alcohols. Some alcohol complexes with acetone and acetonitrile were investigated both in the gas phase and in a continuum of the relevant solvent.

Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method

The performance of quantum mechanical methods on the calculation of protein NMR chemical shifts is reviewed based on the recently developed automatic fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach. By using the Poisson-Boltzmann (PB) model and first solvation water molecules, the influence of solvent effect is also discussed. Benefiting from the fragmentation algorithm, the AF-QM/MM approach is computationally efficient, linear-scaling with a low pre-factor, and thus can be applied to routinely calculate the ab initio NMR chemical shifts for proteins of any size. The results calculated using Density Functional Theory (DFT) show that when the solvent effect is included, this method can accurately reproduce the experimental ¹H NMR chemical shifts, while the ¹³C NMR chemical shifts are less affected by the solvent. However, although the inclusion of solvent effect shows significant improvement for ¹⁵N chemical shifts, the calculated values still have large deviations from the experimental observations. Our study further demonstrates that AF-QM/MM calculated results accurately reflect the dependence of ¹³C(α) NMR chemical shifts on the secondary structure of proteins, and the calculated ¹H chemical shift can be utilized to discriminate the native structure of proteins from decoys.