Modeling solvent effects and convergence of 31P-NMR shielding calculations with COBRAMM

Solvent effects on 31P-NMR parameters for triphenylphosphine oxide and triphenylphosphine in chloroform have been extensively investigated by testing different solvation models. The solvent is described implicitly, mixed implicitly/explicitly, and using full explicit models. Polarizable continuum model (PCM), molecular dynamic (MD) simulations, and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations are used to disclose the effects of solute/solvent interactions and, more generally, the role of the embedding in NMR simulations. The results show the beneficial effect of carrying out QM/MM optimizations on top of geometries directly extracted from classical MD simulations, used to ensure representative conformational sampling. The nuclear shielding convergence has been tested against a different number of snapshots and with the inclusion of solvent shells into the QM region. An automated MD//QM/MM//GIAO protocol, implemented in the COBRAMM package, is here proposed and tested on trimethyl phosphite showing that our approach boosts the convergence of nuclear shielding satisfactorily. The present work aims to be a stepping-stone to assess proper QM/MM computational strategies in simulating chemical shifts in non-homogeneous systems like supramolecular and biological systems.

Benchmark Study on the Calculation of 207Pb NMR Chemical Shifts

A benchmark set for the computation of 207Pb nuclear magnetic resonance (NMR) chemical shifts is presented. The PbS50 set includes conformer ensembles of 50 lead-containing molecular compounds and their experimentally measured 207Pb NMR chemical shifts. Various bonding motifs at the Pb center with up to seven bonding partners are included. Six different solvents were used in the measurements. The respective shifts lie in the range between +10745 and -5030 ppm. Several calculation settings are assessed by evaluating computed 207Pb NMR shifts for the use with different density functional approximations (DFAs), relativistic approaches, treatment of the conformational space, and levels for geometry optimization. Relativistic effects were included explicitly with the zeroth order regular approximation (ZORA), for which only the spin-orbit variant was able to yield reliable results. In total, seven GGAs and three hybrid DFAs were tested. Hybrid DFAs significantly outperform GGAs. The most accurate DFAs are mPW1PW with a mean absolute deviation (MAD) of 429 ppm and PBE0 with an MAD of 446 ppm. Conformational influences are small as most compounds are rigid, but more flexible structures still benefit from Boltzmann averaging. Including explicit relativistic treatments such as SO-ZORA in the geometry optimization does not show any significant improvement over the use of effective core potentials (ECPs).

Evidence of extremely short hydrogen bond in the homoconjugated ferrocene-1,1'-diyl-bisphosphinic acid anion: sign change of the H/D isotope effect on the 31P NMR chemical shift

The structure of the two intramolecular hydrogen-bonded motifs within ferrocene-1,1'-diyl-bisphosphinic acid, a cyclic dimer and a homoconjugated anion, has been experimentally revealed by NMR spectroscopy for a solution in a low-freezing polar aprotic CDF3/CDF2Cl medium at 100 K. Structure elucidation was achieved with the help of the H/D isotope effects on the 1H, 2H and, for the first time, 31P NMR chemical shifts. The questions of bridging hydron localization and origins of opposite signs of H/D isotope effects on the 31P NMR chemical shifts in the cyclic dimer and homoconjugated anion have also been addressed by DFT calculations, including numerical solution of the Schrödinger equation for proton and deuteron vibrations in the anharmonic double well potentials.

31P Nuclear Magnetic Resonance Spectroscopy as a Probe of Thorium-Phosphorus Bond Covalency: Correlating Phosphorus Chemical Shift to Metal-Phosphorus Bond Order

We report the use of solution and solid-state 31P Nuclear Magnetic Resonance (NMR) spectroscopy combined with Density Functional Theory calculations to benchmark the covalency of actinide-phosphorus bonds, thus introducing 31P NMR spectroscopy to the investigation of molecular f-element chemical bond covalency. The 31P NMR data for [Th(PH2)(TrenTIPS)] (1, TrenTIPS = {N(CH2CH2NSiPri3)3}3-), [Th(PH)(TrenTIPS)][Na(12C4)2] (2, 12C4 = 12-crown-4 ether), [{Th(TrenTIPS)}2(μ-PH)] (3), and [{Th(TrenTIPS)}2(μ-P)][Na(12C4)2] (4) demonstrate a chemical shift anisotropy (CSA) ordering of (μ-P)3- > (═PH)2- > (μ-PH)2- > (-PH2)1- and for 4 the largest CSA for any bridging phosphido unit. The B3LYP functional with 50% Hartree-Fock mixing produced spin-orbit δiso values that closely match the experimental data, providing experimentally benchmarked quantification of the nature and extent of covalency in the Th-P linkages in 1-4 via Natural Bond Orbital and Natural Localized Molecular Orbital analyses. Shielding analysis revealed that the 31P δiso values are essentially only due to the nature of the Th-P bonds in 1-4, with largely invariant diamagnetic but variable paramagnetic and spin-orbit shieldings that reflect the Th-P bond multiplicities and s-orbital mediated transmission of spin-orbit effects from Th to P. This study has permitted correlation of Th-P δiso values to Mayer bond orders, revealing qualitative correlations generally, but which should be examined with respect to specific ancillary ligand families rather than generally to be quantitative, reflecting that 31P δiso values are a very sensitive reporter due to phosphorus being a soft donor that responds to the rest of the ligand field much more than stronger, harder donors like nitrogen.

New efficient pecS-n (n = 1, 2) basis sets for quantum chemical calculations of 31P NMR chemical shifts

The basis sets that are used in the quantum chemical calculations of ³¹P NMR chemical shifts have always been one of the most important factors of accuracy. Regardless of what high-quality approach is employed, using basis sets of insufficient flexibility in the important angular regions may give poor results and lead to misassignments of the signals in the ³¹P NMR spectra. In this work, it was found that the existing nonrelativistic basis sets for phosphorus atom of double- and triple-ζ quality, specialized for the ³¹P NMR chemical shifts calculations, are essentially undersaturated in the d-angular space that occurred to play a significant role in the overall accuracy of these calculations. This problem has been thoroughly investigated, and new pecS-n (n = 1, 2) basis sets for phosphorus chemical shifts calculations were proposed. The exponents and contraction coefficients for the pecS-n basis sets were generated with the property-energy consistent method that has been introduced in our earlier paper, and has been proven useful in the creation of efficient property-oriented basis sets. New basis sets were optimized using the GIAO-DFT method with the B97-2 functional. Extensive benchmark calculations showed that the pecS-1 and pecS-2 basis sets provide very good accuracy, characterized by the corrected mean absolute percentage errors against the experiment of about 7.03 and 4.42 ppm, respectively. In particular, the accuracy of ³¹P NMR chemical shifts calculations achieved with the pecS-2 basis set is one of the most favorable accuracies for today. We believe that our new pecS-n (n = 1, 2) basis sets for phosphorus atom will prove useful in modern large-scale quantum chemical calculations of ³¹P NMR chemical shifts.

Computation of CCSD(T)-Quality NMR Chemical Shifts via Δ-Machine Learning from DFT

NMR spectroscopy undoubtedly plays a central role in determining molecular structures across different chemical disciplines, and the accurate computational prediction of NMR parameters is highly desirable. In this work, a new Δ-machine learning approach is presented to correct DFT-computed NMR chemical shifts using input features from the calculation and in addition highly accurate reference data at the CCSD(T)/pcSseg-2 level of theory with a basis set extrapolation scheme. The model is trained on a data set containing 1000 optimized and geometrically distorted structures of small organic molecules comprising most elements of the first three periods and containing data for 7090 ¹H and 4230 ¹³C NMR chemical shifts. Applied to the PBE0/pcSseg-2 method, the mean absolute deviation (MAD) on the internal NMR shift test set is reduced by 81% for ¹H and 92% for ¹³C at virtually no additional computational cost. For 12 different DFT functional and basis set combinations, the MAD of the ML-corrected NMR shifts ranges from 0.021 to 0.039 ppm (¹H) and from 0.38 to 1.07 ppm (¹³C). Importantly, the new method consistently outperforms the simple and widely used linear regression correction technique. This behavior is reproduced on three different external benchmark sets, confirming the generality and robustness of the correction scheme, which can easily be applied in DFT-based spectral simulations.

Cationic Phosphinidene as a Versatile P1 Building Block: [LC-P]+ Transfer from Phosphonio-Phosphanides [LC-P-PR3]+ and Subsequent LC Replacement Reactions (LC = N-Heterocyclic Carbene)

Cationic imidazoliumyl(phosphonio)-phosphanides [LC-P-PR3]+ (1a-e+, LC = 4,5-dimethyl-1,3-diisopropylimidazolium-2-yl; R = alkyl, aryl) are obtained via the nucleophilic fragmentation of tetracationic tetraphosphetane [(LC-P)4][OTf]4 (2[OTf]4) with tertiary phosphanes. They act as [LC-P]+ transfer reagents in phospha-Wittig-type reactions, when converted with various thiocarbonyls, giving unprecedented cationic phosphaalkenes [LC-P═CR2]+ (5a-f[OTf]) or phosphanides [LC-P-CR(NR2')]+ (6a-d[OTf]). Theoretical calculations suggest that three-membered cyclic thiophosphiranes are crucial intermediates of this reaction. To test this hypothesis, treatment of [LC-P-PPh3]+ with phosphaalkenes, that are isolobal to thioketones, permits the isolation of diphosphirane salts 11a,b[OTf]. Furthermore, preliminary studies suggest that the cationic phosphaalkene [LC-P═CPh2]+ may be employed to access rare examples of η2-P═C π-complexes with Pd0 and Pt0 when treated with [Pd(PPh3)4] and [Pt(PPh3)3] for which analogous complexes of neutral phosphaalkenes are scarce. The versatility of [LC-P]+ as a valuable P1 building block was showcased in substitution reactions of the transferred LC-substituent using nucleophiles. This is demonstrated through the reactions of 5a[OTf] and 6c[OTf] with Grignard reagents and KNPh2, providing a convenient, high-yielding access to MesP═CPh2 (16) and otherwise difficult-to-synthesize 1,3-diphosphetane 17 and P-aminophosphaalkenes.

Stereochemical Study of the Super Large Tetrakis Alkaloid Alasmontamine A by Means of an Advanced Computational NMR

1H and 13C NMR chemical shifts of the tetrakis monoterpene indole alkaloid alasmontamine A, with a molecular formula of C84H91N8O12, have been calculated within the DFT framework. Six minimum energy conformers of this alkaloid were identified, and three key configurations that contribute to its NMR shielding constants were established. Several ambiguities in the reported assignment of the NMR chemical shifts of alasmontamine A have been resolved.

Combined computational and experimental study about the incorporation of phosphorus into the structure of graphene oxide

Phosphorus-containing graphene-based hybrids are materials with outstanding properties for diverse applications. In this work, an easy route to produce phosphorus-graphene oxide hybrid materials is described, involving the use of variable amounts of H₃PO₄ and H₂SO₄ during the reaction of oxidation of a graphitic precursor. The physical and chemical features of the hybrids change significantly with the variation in the acid amounts used in the syntheses. XPS and solid-state ¹³C and ³¹P NMR results show that the hybrids contain large amounts of oxygen functional groups, with the phosphorus incorporation proceeding mostly through the formation of phosphate-like linkages and other functions with C-O-P bonds. The experimental findings are supported by DFT calculations, which allow the assessment of the energetics and the geometry of the interaction between phosphate groups and graphene-based models; these calculations are also used to predict the chemical shifts in the ³¹P and ¹³C NMR spectra of the models, which show good agreement with the experimentally observed solid-state NMR spectra.

Improving the accuracy of 31P NMR chemical shift calculations by use of scaling methods

Calculation of ³¹P NMR chemical shifts for a series of tri- and tetracoordinate phosphorus compounds using several basis sets and density functional theory (DFT) functionals gave a modest fit to experimental chemical shifts, but an excellent linear fit when plotted against the experimental values. The resultant scaling methods were then applied to a variety of "large" compounds previously selected by Latypov et al. and a set of stereoisomeric and unusual compounds selected here. No one method was best for all structural types. For compounds that contain P-P bonds and P-C multiple bonds, the Latypov et al. method using the PBE0 functional was best (mean absolute deviation/root mean square deviation (MAD/RMSD) = 6.9/8.5 ppm and 6.6/8.2 ppm, respectively), but for the full set of compounds gave higher deviations (MAD/RMSD = 8.2/12.3 ppm), and failed by over 60 ppm for a three-membered phosphorus heterocycle. Use of the M06-2X functional for both the structural optimization and NMR chemical shift calculation was best overall for the compounds without P-C multiple bonds (MAD/RMSD = 5.4/7.1 ppm), but failed by 30-49 ppm for compounds having any P-C multiple-bond character. Failures of these magnitudes have not been reported previously for these widely used functionals. These failures were then used to screen a variety of recommended functionals, leading to better overall methods for calculation of these chemical shifts: optimization with the M06-2X functional and NMR calculation with the PBE0 or ωB97x-D functionals gave values for MAD/RMSD = 6.9/8.5 ppm and 6.8/9.1 ppm, respectively, over an experimental chemical shift range of -181 to 356 ppm. Due to the unexplained failures observed, we recommend use of more than one method when looking at novel structures.

Organophosphorus Azoles Incorporating a Tetra-, Penta-, and Hexacoordinated Phosphorus Atom: NMR Spectroscopy and Quantum Chemistry

The review presents extensive data (from the author's work and the literature) on the stereochemical structure of functionalized organophosphorus azoles (pyrroles, pyrazoles, imidazoles and benzazoles) and related compounds, using multinuclear ¹H, ¹³C, ³¹P NMR spectroscopy and quantum chemistry. ³¹P NMR spectroscopy, combined with high-level quantum-chemical calculations, is the most convenient and reliable approach to studying tetra-, penta-, and hexacoordinated phosphorus atoms of phosphorylated N-vinylazoles and evaluating their Z/E isomerization.

Application of the oxycodone templated molecular imprinted polymer in adsorption of the drug from human blood plasma as the real biological environment; a joint experimental and density functional theory study

In this project, we have synthesized and used a molecular imprinted polymer (MIP) for adsorption of oxycodone residue from the biological samples. Indeed, this study aims to develop a suitable method for determination of oxycodone drug residue in the human plasma using the common analysis methods. Therefore, the MIP was used for the solid phase extraction (MIP-SPE) approach in order to collect the oxycodone opioid and to concentrate it in the blood plasma samples. The extraction parameters such as adsorption time, pH, and the amount of sorbent in blood plasma were optimized and the capacity of loading amount (LA) for adsorbing it was determined. Moreover, a high performance liquid chromatography (HPLC)-UV detector method was validated and used for analyzing of the mentioned opioid extracted from plasma. The results showed that the limit of detection (LOD), and the limit of quantization (LOQ) for the developed MIP-SPE method were 1.24 ppb, and 3.76 ppb, respectively. Moreover, both of the MIP-, and non-imprinted polymers (NIP)-drug complexes were designed and were then optimized by the density functional theory (DFT) method. The results showed that the theoretical calculations supported the experimental data, confirming the favorability of adsorption of the drug by MIP compared to NIP.

Reactivity of Perhalogenated Octahedral Phospha- and Arsaboranes toward THF: A Joint Experimental/Computational Study

Reactions of the perhalogenated polyhedral pnictogenaboranes closo-1,2-Pn₂B₄Hal₄ (Pn = P, As; Hal = Cl, Br) with Lewis bases are presently being studied with a focus on rationalizing the sites of nucleophilic attacks on clusters bearing σ-holes. These σ-holes are localized both on pnictogens and, for Hal = Br, on bromine atoms, as revealed by electrostatic potential (ESP) and intrinsic bond orbital (IBO) analyses. Surprisingly, the attack of the cyclic ether THF on closo-1,2-Pn₂B₄Br₄ does not occur on the site with the largest positive partial charge, centered in the middle of the pnictogen-pnictogen vector. Instead, presumably promoted by the positivated bromine substituents, THF inserts into the boron-bromine bonds of the negatively charged boron atoms opposite to the pnictogen atoms to form 4-(4-bromobut-1-oxy)-closo-1,2-Pn₂B₄Br₃ (1-PB and 1-AsB) and 4,6-(4-bromobut-1-oxy)₂-closo-1,2-Pn₂B₄Br₂ (2-PB and 2-AsB). ¹¹B and ³¹P chemical shift computations at various levels support the assignments of the signals, which reflect the correctness of the molecular geometries in solutions. The Lewis-acidic perchlorinated analogues closo-1,2-P₂B₄Cl₄, closo-1,2-As₂B₄Cl₄, and the mixed closo-1,2-AsPB₄Cl₄ bear negative charges. These negative charges are revealed by the V_s,max values when computing the electrostatic potentials both on the boron and the chlorine atoms. Due to this negative charge, the analogues do not react with THF unless they are heated above 66 °C, where they slowly decompose to borate esters B(OR)₃ without the formation of concrete intermediates. The evaluation of ³¹P NMR data of 1-PB has allowed the experimental determination of the coupling constant ¹J(³¹P(1), ³¹P(2)) = |143| Hz in a closo-diphosphaborane for the first time, which agrees well with the computed value of -178 Hz. The pioneering joint experimental vs computational interpretation of ³¹P NMR spectra in the area of boron cluster chemistry was decisive for the structural characterization of 1-PB and 2-PB.

Dual Reactivity of a Geometrically Constrained Phosphenium Cation

A geometrically constrained phosphenium cation in bis(pyrrolyl)pyridine based NNN pincer type ligand (1⁺) was synthesized, isolated and its preliminary reactivity was studied with small molecules. 1⁺ reacts with MeOH and Et₂NH, activating the O−H and N−H bonds via a P‐center/ligand assisted path. The reaction of 1⁺ with one equiv. of H₃NBH₃ leads to its dehydrogenation producing 5. Interestingly, reaction of 1⁺ with an excess H₃NBH₃ leads to phosphinidene (P^I) species coordinating to two BH₃ molecules (6). In contrast, [1⁺][OTf] reacts with Et₃SiH by hydride abstraction yielding 1‐H and Et₃SiOTf, while [1⁺][B(C₆F₅)₄] reacts with Et₃SiH via an oxidative addition type reaction of Si−H bond to P‐center, affording a new P^V compound (8). However, 8 is not stable over time and degrades to a complex mixture of compounds in matter of minutes. Despite this, the ability of [1⁺][B(C₆F₅)₄] to activate Si−H bond could still be tested in catalytic hydrosilylation of benzaldehyde, where 1⁺ closely mimics transition metal behaviour.

Taming phosphorus mononitride

Phosphorus mononitride (PN) only has a fleeting existence on Earth, and molecular precursors for the release of this molecule under mild conditions in solution have remained elusive. Here we report the synthesis of an anthracene-based precursor-an anthracene moiety featuring an azidophosphine bridge across its central ring-that dissociates into dinitrogen, anthracene and P≡N in solution with a first-order half-life of roughly 30 min at room temperature. Heated under reduced pressure, this azidophosphine-anthracene precursor decomposes in an explosive fashion at around 42 °C, as demonstrated in a molecular-beam mass spectrometry study. The precursor is also shown to serve as a PN transfer reagent in the synthesis of an Fe-NP coordination complex, through ligand exchange with its Fe-N₂ counterpart. The terminal N-bonded complex was found to be energetically preferred, compared to its P-bonded linkage isomer, owing to a significant covalent Fe-pnictogen bond character and an associated less unfavourable Pauli repulsion in the metal-ligand interaction.

A phosphonic acid anion and acid dimer dianion stabilized by proton transfer in OHN hydrogen bonds - models of structural motifs in blend polymer membranes

The structure of intermolecular hydrogen-bonded complexes formed between tert-butylphosphonic acid and trimethylpyridine molecules has been experimentally studied as the simplest model system of the structural motifs in blend proton-conducting polymer membranes based on phosphonic acid residues. The stoichiometry of the formed complexes and proton positions in OHO and OHN hydrogen bonds were established by the H/D isotope effects and temperature dependences of the signals in ¹H and ³¹P NMR spectra. Two structural motifs, namely, 1 : 2 and 2 : 2 acid-base complexes, were identified at the low temperature in a polar aprotic environment. In the 1 : 2 complex, one proton has passed through the hydrogen bond center creating a chain of two cooperatively coupled OHN bonds, while in the 2 : 2 complex both OHN bonds are zwitterionic and anti-cooperatively coupled to each other via a dianionic cyclic dimer of phosphonic acid in the middle. The dianionic cyclic dimer is metastable by itself, but under the used experimental conditions it is stabilized by complexation with two trimethylpyridinium cations. Additionally, quantum chemical calculations using the DFT method were carried out to support the experimental data.

Recent advances in the chemistry of the phosphaethynolate and arsaethynolate anions

Over the past decade, the reactivity of 2-phosphaethynolate (OCP^-), a heavier analogue of the cyanate anion, has been the subject of momentous interest in the field of modern organometallic chemistry. It is used as a precursor to novel phosphorus-containing heterocycles and as a ligand in decarbonylative processes, serving as a synthetic equivalent of a phosphinidene derivative. This perspective aims to describe advances in the reactivities of phosphaethynolate and arsaethynolate anions (OCE^-; E = P, As) with main-group element, transition metal, and f-block metal scaffolds. Further, the unique structures and bonding properties are discussed based on spectroscopic and theoretical studies.

Benchmark Study on the Calculation of 119Sn NMR Chemical Shifts

A new benchmark set termed SnS51 for assessing quantum chemical methods for the computation of ¹¹⁹Sn NMR chemical shifts is presented. It covers 51 unique ¹¹⁹Sn NMR chemical shifts for a selection of 50 tin compounds with diverse bonding motifs and ligands. The experimental reference data are in the spectral range of ±2500 ppm measured in seven different solvents. Fifteen common density functional approximations, two scalar- and one spin-orbit relativistic approach are assessed based on conformer ensembles generated using the CREST/CENSO scheme and state-of-the-art semiempirical (GFN2-xTB), force field (GFN-FF), and composite DFT methods (r²SCAN-3c). Based on the results of this study, the spin-orbit relativistic method combinations of SO-ZORA with PBE0 or revPBE functionals are generally recommended. Both yield mean absolute deviations from experimental data below 100 ppm and excellent linear regression determination coefficients of ≤0.99. If spin-orbit calculations are not affordable, the use of SR-ZORA with B3LYP or X2C with ωB97X or M06 may be considered to obtain qualitative predictions if no severe spin-orbit effects, for example, due to heavy nuclei containing ligands, are expected. An empirical linear scaling correction is demonstrated to be applicable for further improvement, and respective empirical parameters are given. Conformational effects on chemical shifts are studied in detail but are mostly found to be small. However, in specific cases when the ligand sphere differs substantially between conformers, chemical shifts can change by up to several hundred ppm.

Phosphine oxides as NMR and IR spectroscopic probes for geometry and energy of PO···H–A hydrogen bonds

In this work we evaluate the possibility to use the NMR and IR spectral properties of P=O group to estimate the geometry and strength of hydrogen bonds which it forms...

What Distinguishes the Strength and the Effect of a Lewis Acid: Analysis of the Gutmann-Beckett Method

IUPAC defines Lewis acidity as the thermodynamic tendency for Lewis pair formation. This strength property was recently specified as global Lewis acidity (gLA), and is gauged for example by the fluoride ion affinity. Experimentally, Lewis acidity is usually evaluated by the effect on a bound molecule, such as the induced ³¹ P NMR shift of triethylphosphine oxide in the Gutmann-Beckett (GB) method. This type of scaling was called effective Lewis acidity (eLA). Unfortunately, gLA and eLA often correlate poorly, but a reason for this is unknown. Hence, the strength and the effect of a Lewis acid are two distinct properties, but they are often granted interchangeably. The present work analyzes thermodynamic, NMR specific, and London dispersion effects on GB numbers for 130 Lewis acids by theory and experiment. The deformation energy of a Lewis acid is identified as the prime cause for the critical deviation between gLA and eLA but its correction allows a unification for the first time.

Reactivity of the pentelidene complexes [Cp*E{W(CO)5}2] (E = P, As) towards dichalcogenides and chalcogenols - synthesis of novel chalcogenopentelidene complexes

Pentelidene complexes of the type [Cp*E{W(CO)₅}₂] (Cp* = C₅Me₅; 1a: E = P, 1b: E = As) were reacted with the dichalcogenides R₂Ch₂ (R = Ph, Mes, Tipp; Ch = S, Se, Te; Mes = 2,4,6-trimethylphenyl; Tipp = 2,4,6-triisopropylphenyl) and the chalcogenols PhChH (Ch = S, Se). It has been shown that the formation of new E-Ch bonds proceeds under elimination of the Cp* substituent. The resulting chalcogenopentelidene complexes, which have been isolated and fully characterised, represent a novel class of phosphinidene complexes which can be synthesised through this general synthetic route.

A general QSPR protocol for the prediction of atomic/inter-atomic properties: a fragment based graph convolutional neural network (F-GCN)

In this study, a general quantitative structure-property relationship (QSPR) protocol, fragment based graph convolutional neural network (F-GCN), was developed for the prediction of atomic/inter-atomic properties. We applied this novel artificial intelligence (AI) tool in predictions of NMR chemical shifts and bond dissociation energies (BDEs). The obtained results were comparable to experimental measurements, while the computational cost was substantially reduced, with respect to pure density functional theory (DFT) calculations. The two important features of F-GCN can be summarised as: first, it could utilise different levels of molecular fragments for atomic/inter-atomic information extraction; second, the designed architecture is also open to include additional descriptors for a more accurate solution of the local environment at atomic level, making itself more efficient for structural solutions. And during our test, the averaged prediction error of 1H NMR chemical shifts is as small as 0.32 ppm, and the error of C-H BDE estimation is 2.7 kcal mol-1. Moreover, we further demonstrated the applicability of this developed F-GCN model via several challenging structural assignments. The success of the F-GCN in atomic and inter-atomic predictions also indicates an essential improvement of computational chemistry with the assistance of AI tools.

Quantum Chemistry Calculations for Metabolomics

A primary goal of metabolomics studies is to fully characterize the small-molecule composition of complex biological and environmental samples. However, despite advances in analytical technologies over the past two decades, the majority of small molecules in complex samples are not readily identifiable due to the immense structural and chemical diversity present within the metabolome. Current gold-standard identification methods rely on reference libraries built using authentic chemical materials ("standards"), which are not available for most molecules. Computational quantum chemistry methods, which can be used to calculate chemical properties that are then measured by analytical platforms, offer an alternative route for building reference libraries, i.e., in silico libraries for "standards-free" identification. In this review, we cover the major roadblocks currently facing metabolomics and discuss applications where quantum chemistry calculations offer a solution. Several successful examples for nuclear magnetic resonance spectroscopy, ion mobility spectrometry, infrared spectroscopy, and mass spectrometry methods are reviewed. Finally, we consider current best practices, sources of error, and provide an outlook for quantum chemistry calculations in metabolomics studies. We expect this review will inspire researchers in the field of small-molecule identification to accelerate adoption of in silico methods for generation of reference libraries and to add quantum chemistry calculations as another tool at their disposal to characterize complex samples.

Sensitivity of 31 P NMR chemical shifts to hydrogen bond geometry and molecular conformation for complexes of phosphinic acids with pyridines

The results of the quantum-chemical investigation of a series of hydrogen-bonded 1:1 acid-base complexes formed by model phosphinic acids, Me₂ POOH, and PhHPOOH, are reported. A series of substituted pyridines (pK_a range from 0.5 to 10) was chosen as proton acceptors. Gradual changes of isotropic ³¹ P nuclear magnetic resonance (NMR) chemical shift, δP, were correlated with the bridging proton position in the intermolecular OHN hydrogen bond, namely, r (OH) distance; the proposed correlation could easily be extended to other phosphinic acids as well. For complexes with pyridine and 2,4,6-trimethylpyridine, we have investigated in more detail several factors influencing the δP values: (1) the proton transfer within the OHN hydrogen bond; (2) the rotation of the pyridine ring around the hydrogen bond axis (associated with the formation/breakage of additional weak PO···H-C hydrogen bond); and (3) the rotation of the phenyl substituent in phenylphosphinic acid around the P-C axis. All these factors appeared to be of similar magnitude, thus masking their individual contributions that have to be independently estimated for a reliable spectral interpretation.

Defect-Assisted Loading and Docking Conformations of Pharmaceuticals in Metal-Organic Frameworks

Understanding of drug-carrier interactions is essential for the design and application of metal-organic framework (MOF)-based drug-delivery systems, and such drug-carrier interactions can be fundamentally different for MOFs with or without defects. Herein, we reveal that the defects in MOFs play a key role in the loading of many pharmaceuticals with phosphate or phosphonate groups. The host-guest interaction is dominated by the Coulombic attraction between phosphate/phosphonate groups and defect sites, and it strongly enhances the loading capacity. For similar molecules without a phosphate/phosphonate group or for MOFs without defects, the loading capacity is greatly reduced. We employed solid-state NMR spectroscopy and molecular simulations to elucidate the drug-carrier interaction mechanisms. Through a synergistic combination of experimental and theoretical analyses, the docking conformations of pharmaceuticals at the defects were revealed.

Self-Assembly of Hydrogen-Bonded Cage Tetramers of Phosphonic Acid

The self-association of phosphonic acids with general formula RP(O)(OH)2 in solution state remains largely unexplored. The general understanding is that such molecules form multiple intermolecular hydrogen bonds, but the stoichiometry of self-associates and the bonding motifs are unclear. In this work, we report the results of the study of self-association of tert-butylphosphonic acid using low temperature liquid-state 1H and 31P NMR spectroscopy (100 K; CDF3/CDF2Cl) and density functional theory (DFT) calculations. For the first time, we demonstrate conclusively that polar aprotic medium tert-butylphosphonic acid forms highly symmetric cage-like tetramers held by eight OHO hydrogen bonds, which makes the complex quite stable. In these associates. each phosphonic acid molecule is bonded to three other molecules by forming two hydrogen bonds as proton donor and two hydrogen bonds as proton acceptor. Though the structure of such cage-like tetramers is close to tetrahedral, the formal symmetry of the self-associate is C2.

Comprehensive Benchmark Study on the Calculation of 29Si NMR Chemical Shifts

A comprehensive and diverse benchmark set for the calculation of ²⁹Si NMR chemical shifts is presented. The SiS146 set includes 100 silicon containing compounds with 146 experimentally determined reference ²⁹Si NMR chemical shifts measured in nine different solvents in a range from -400 to +828 ppm. Silicon atoms bound to main group elements as well as transition metals with coordination numbers of 2-6 in various bonding patterns including multiple bonds and coordinative and aromatic bonding are represented. The performance of various common and specialized density functional approximations including (meta-)GGA, hybrid, and double-hybrid functionals in combination with different AO basis sets and for differently optimized geometries is evaluated. The role of scalar-relativistic effects is further investigated by inclusion of the zeroth order regular approximation (ZORA) method into the calculations. GGA density functional approximations (DFAs) are found to outperform hybrid DFAs with B97-D3 performing best with an MAD of 7.2 ppm for the subset including only light atoms (Z < 18), while TPSSh is the best tested hybrid functional with an MAD of 10.3 ppm. For ²⁹Si cores in the vicinity of heavier atoms, the application of ZORA proved indispensable. Inclusion of spin-orbit effects into the ²⁹Si NMR chemical shift calculation decreases the mean absolute deviations by up to 74% compared to calculations applying effective core potentials.

Toward Accurate Predictions of Atomic Properties via Quantum Mechanics Descriptors Augmented Graph Convolutional Neural Network: Application of This Novel Approach in NMR Chemical Shifts Predictions

In this study, an augmented Graph Convolutional Network (GCN) with quantum mechanics (QM) descriptors was reported for its accurate predictions of NMR chemical shifts with respect to experimental values. The prediction errors of ¹³C/¹H NMR chemical shifts can be as small as 2.14/0.11 ppm. There are two crucial characteristics for this modified GCN: in one aspect, such a novel neural network could efficiently extract the overall molecule structure information; in another aspect, it could accurately solve the chemical environment of the target atom. As there exists an imperfect linear regression between the experimental NMR chemical shifts (δ) and the density functional theory (DFT) calculated isotropic shielding constants (σ), the inclusion of QM descriptors within GCN can largely improve its performance. Moreover, few-shot learning also becomes feasible with these descriptors. The success of this novel GCN in chemical shifts predictions also indicates its potential applicability for other computational studies.

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.

Phosphine Oxides as Spectroscopic Halogen Bond Descriptors: IR and NMR Correlations with Interatomic Distances and Complexation Energy

An extensive series of 128 halogen-bonded complexes formed by trimethylphosphine oxide and various F-, Cl-, Br-, I- and At-containing molecules, ranging in energy from 0 to 124 kJ/mol, is studied by DFT calculations in vacuum. The results reveal correlations between R–X⋅⋅⋅O=PMe₃ halogen bond energy ΔE, X⋅⋅⋅O distance r, halogen’s σ-hole size, QTAIM parameters at halogen bond critical point and changes of spectroscopic parameters of phosphine oxide upon complexation, such as ³¹P NMR chemical shift, ΔδP, and P=O stretching frequency, Δν. Some of the correlations are halogen-specific, i.e., different for F, Cl, Br, I and At, such as ΔE(r), while others are general, i.e., fulfilled for the whole set of complexes at once, such as ΔE(ΔδP). The proposed correlations could be used to estimate the halogen bond properties in disordered media (liquids, solutions, polymers, glasses) from the corresponding NMR and IR spectra.

Asymmetric 1,3-dipolar cycloaddition reaction of chiral 1-alkyl-1,2-diphospholes with diphenyldiazomethane

The 1,3-dipolar cycloaddition of chiral 1-alkyl-1,2-diphosphacyclopenta-2,4-dienes ((1-(−)-menthyl)oxymethyl-1,2-diphosphole and 1-(+)-neomenthyl-1,2-diphosphole) with diphenyldiazomethane leads to novel P-chiral bicyclic phosphiranes having six chiral centers. The degree of diastereoselectivity depends on the substituent at phosphorus, and dramatically increases in the case of (+)-neomenthyl group (de up to 71%). DFT calculations indicate that the cycloaddition is thermodynamically controlled.

The 1,3-dipolar cycloaddition of chiral 1-alkyl-1,2-diphosphacyclopenta-2,4-dienes with diphenyldiazomethane leads to novel P-chiral bicyclic phosphiranes having six chiral centers.

Quantum chemical calculations of 31P NMR chemical shifts of P-donor ligands in platinum(II) complexes

This work aims to find the most suitable method that is practically applicable for the calculation of ³¹P NMR chemical shifts of Pt(II) complexes. The influence of various all-electron and ECP basis sets, DFT functionals, and solvent effects on the optimized geometry was tested. A variety of combinations of DFT functionals BP86, B3LYP, PBE0, TPSSh, CAM-B3LYP, and ωB97XD with all-electron basis sets 6-31G, 6-31G(d), 6-31G(d,p), 6-311G(d,p), and TZVP and ECP basis sets SDD, LanL2DZ, and CEP-31G were used. Chemical shielding constants were then calculated using BP86, PBE0, and B3LYP functionals in combination with the TZ2P basis. The magnitude of spin-orbit interactions was also evaluated.

Phosphorene and Black Phosphorus: The 31P NMR View

This work aims at characterizing for the first time the ³¹P spin interactions determining the nuclear magnetic resonance (NMR) properties of solid black phosphorus (bP) and of its few-layer exfoliated form (fl-bP). Indeed, the knowledge of these properties is still very poor, despite the great interest received by this layered phosphorus allotrope and its exfoliated 2D form, phosphorene. By combining density functional theory (DFT) calculations and solid-state NMR experiments on suspensions of fl-bP nanoflakes and on solid bP, it has been possible to characterize the ³¹P homonuclear dipolar and chemical shift interactions, identifying the network of ³¹P nuclei more strongly dipolarly coupled and highlighting two kinds of magnetically nonequivalent ³¹P nuclei. These results add an important missing piece of information to the fundamental chemico-physical knowledge of bP and support future extensive applications of NMR spectroscopy to the characterization of phosphorene-based materials.

Conformational Mobility and Proton Transfer in Hydrogen-Bonded Dimers and Trimers of Phosphinic and Phosphoric Acids

The monomers, H-bonded cyclic dimers, and trimers of five acids were studied by density functional theory calculations, such as hypophosphorous acid (H₂POOH, 1), dimethylphosphinic acid (Me₂POOH, 2), phenylphosphinic acid (PhHPOOH, 3), dimethylphosphoric acid ((MeO)₂POOH, 4), and diphenylphosphoric acid ((PhO)₂POOH, 5). Particular attention was paid to the conformational manifold existing due to the internal degrees of freedom: proton transfer (PT), puckering ("twist") within the ring of H-bonds, and mobility of the substituents (namely, -Ph, -OMe, and -OPh rotations). For acid 3, the number of conformers is additionally increased because of the varying relative orientation of nonequivalent substituents in cyclic complexes. We show that ³¹P NMR chemical shifts (δP) are very sensitive to the details of the conformation, spanning ranges from ca. 1 ppm (for trimers of acids 1 and 2) to ca. 12 ppm (for trimers of 4). The energy barriers for the transitions between conformers are rather low (<6 kcal/mol for PTs, <2.5 kcal/mol for puckerings, and ca. <3 kcal/mol for rotations of substituents), such that the fast exchange regime in the NMR timescale and subsequent δP averaging are expected. Correlations are proposed linking the change of average δP with the H-bond energy, showing the slope of ca. 4 ppm per kcal/mol. The sensitivity of δP to the OPO angle and the OPOH dihedral angle and the geometries of both H-bonds formed by the POOH moiety are analyzed.

Formation of an imidazoliumyl-substituted [(LC)4P4]4+ tetracation and transition metal mediated fragmentation and insertion reaction (LC = NHC)

Tetracationic cyclo-tetraphosphane [(L_C)₄P₄]⁴⁺ as triflate salt (3[OTf]₄) (L_C = 4,5-dimethyl-1,3-diisopropyl-imidazol-2-yl) is obtained in high yield from the reduction of [L_CPCl₂]⁺ (4[OTf]) with 1,4-bis(trimethylsilyl)-1,4-dihydropyrazine (6) and represents the first salt of the cationic cyclo-phosphane series with the general formula [L _n P _n ] ⁿ⁺. Theoretical calculations reveal the electrophilic nature of the P atoms within the P₄-ring due to the influence of the imidazoliumyl-substituents. Further reduction of 3[OTf]₄ with 6 affords the unexpected formation of the notricyclane P₇-type cation [(L_C)₃P₇]³⁺ (9[OTf]₃). Selective transition metal mediated [2 + 2]-fragmentation of 3 ⁴⁺ is achieved when 3[OTf]₄ is reacted with Fe₂(CO)₉, Pd(PPh₃)₄ and Pt(PPh₃)₄ leading to the formation of the dicationic diphosphene complexes [(η²-L_CP[double bond, length as m-dash]PL_C)Fe(CO)₄]²⁺ (12[OTf]₂) and [(η²-L_CP[double bond, length as m-dash]PL_C)M(PPh₃)₂]²⁺ (13[OTf]₂ for M = Pd; 14[OTf]₂ for M = Pt). In contrast, the reaction of 3[OTf]₄ with an excess of AuCl(tht) gives rise to the formation of the five-membered ring complex [((L_C)₄P₄)AuCl₂]³⁺ (15[OTf]₃), where the Au(i) atom reductively inserts into a P-P bond of 3 ⁴⁺.

P-Chiral 1,7-diphosphanorbornenes: from asymmetric phospha-Diels-Alder reactions towards applications in asymmetric catalysis

A straightforward synthesis of P-chiral polycyclic phosphines by an asymmetric Diels-Alder reaction of 1-alkyl-1,2-diphospholes and (5R)-(l-menthyloxy)-2(5H)-furanone (MOxF) is presented. The [4 + 2] cycloaddition reaction of 1,2-diphospholes 1-3 with MOxF (4) proceeded with high diastereoselectivity (de up to 90%) resulting in the corresponding enantiopure anti-endo-1,7-diphosphanorbornenes 5a-7a. The absolute configuration of 5-7 was proved by a variety of 1D/2D NMR correlation methods. The use of the anti-endo-1,7-diphosphanorbornene 5a in the Pd-catalyzed asymmetric allylic alkylation of cinnamyl acetate 8 with cyclic β-ketoesters 9a,b provided up to 52% ee.