A review on point mutations via proton transfer in DNA base pairs in the absence and presence of electric fields

This comprehensive review focuses on spontaneous mutations that may occur during DNA replication, the fundamental process responsible for transferring genetic information. In 1963, Löwdin postulated that these mutations are primarily a result of proton transfer reactions within the hydrogen-bonded DNA base pairs. The single and double proton transfer reactions within the base pairs in DNA result in zwitterions and rare tautomers, respectively. For persistent mutations, these products must be generated at high rates and should be thermodynamically stable. This review covers the proton transfer reactions studied experimentally and computationally. The review also examines the influence of externally applied electric fields on the thermodynamics and kinetics of proton transfer reactions within DNA base pairs, and their biological implications.

Polymorph Identification for Flexible Molecules: Linear Regression Analysis of Experimental and Calculated Solution- and Solid-State NMR Data

The Δδ regression approach of Blade et al. [ J. Phys. Chem. A 2020, 124(43), 8959-8977] for accurately discriminating between solid forms using a combination of experimental solution- and solid-state NMR data with density functional theory (DFT) calculation is here extended to molecules with multiple conformational degrees of freedom, using furosemide polymorphs as an exemplar. As before, the differences in measured 1H and 13C chemical shifts between solution-state NMR and solid-state magic-angle spinning (MAS) NMR (Δδexperimental) are compared to those determined by gauge-including projector augmented wave (GIPAW) calculations (Δδcalculated) by regression analysis and a t-test, allowing the correct furosemide polymorph to be precisely identified. Monte Carlo random sampling is used to calculate solution-state NMR chemical shifts, reducing computation times by avoiding the need to systematically sample the multidimensional conformational landscape that furosemide occupies in solution. The solvent conditions should be chosen to match the molecule's charge state between the solution and solid states. The Δδ regression approach indicates whether or not correlations between Δδexperimental and Δδcalculated are statistically significant; the approach is differently sensitive to the popular root mean squared error (RMSE) method, being shown to exhibit a much greater dynamic range. An alternative method for estimating solution-state NMR chemical shifts by approximating the measured solution-state dynamic 3D behavior with an ensemble of 54 furosemide crystal structures (polymorphs and cocrystals) from the Cambridge Structural Database (CSD) was also successful in this case, suggesting new avenues for this method that may overcome its current dependency on the prior determination of solution dynamic 3D structures.

In Situ Monitoring of Competitive Coformer Exchange Reaction by 1H MAS Solid-State NMR

In a competitive coformer exchange reaction, a recent topic of interest in pharmaceutical research, the coformer in a pharmaceutical cocrystal is exchanged with another coformer that is expected to form a cocrystal that is more stable. There will be a competition between coformers to form the most stable product through the formation of hydrogen bonds. This will cause destabilization of the pharmaceutical products during processing or storage. Therefore, it is important to develop a mechanistic understanding of this transformation by monitoring each and every step of the reaction, employing a technique such as 1H nuclear magnetic resonance (NMR). In this study, an in situ monitoring of a coformer exchange reaction is carried out by 1H magic angle spinning (MAS) solid-state NMR (SSNMR) at a spinning frequency of 60 kHz. The changes in caffeine maleic acid cocrystals on addition of glutaric acid and caffeine glutaric cocrystals on addition of maleic acid were monitored. In all of the reactions, it has been observed that caffeine glutaric acid Form I is formed. When glutaric acid was added to 2:1 caffeine maleic acid, the formation of metastable 1:1 caffeine glutaric acid Form I was observed at the start of the experiment, indicating that the centrifugal pressure is enough for the formation. The difference in the end product of the reactions with a similar reaction pathway of 1:1 and 2:1 reactant stoichiometry indicates that a complete replacement of maleic acid has occurred only in the 1:1 stoichiometry of the reactants. The polymorphic transition of caffeine glutaric acid Form II to Form I at higher temperatures was a crucial reason that triggered the exchange of glutaric acid with maleic acid in the reaction of caffeine glutaric acid and maleic acid. Our results are novel since the new reaction pathways in competitive coformer exchange reactions enabled understanding the remarkable role of stoichiometry, polymorphism, temperature, and centrifugal pressure.

Modified air-Fenton with MIL-88A for chemical oxygen demand treatment in used coolant oil

Coolant oil from auto part manufacturing contains additives resulting in high chemical oxygen demand (COD) in wastewater. In this study, COD treatment of coolant oil was investigated in a metal-organic framework (MOF) with MIL-88A by a modified air-Fenton (MAF) process by varying synthetic coolant oil concentrations (1-5%), pH (3-9), air-flow rate (1-2 L/min), amount of MIL-88A (0.2-1.0 g), and reaction time (30-180 min). The results were analyzed using central composite design (CCD) and response surface methodology (RSM) using Minitab ver. 19. The characteristic MIL-88A was characterized by XRD that showed a spindle-like shape with 2θ at 10.2° and 13.0°. The FTIR spectrum revealed the vibrational frequencies at Fe-O (564 cm-1), C-O (1391 and 1600 cm-1), and C = O (1216 and 1710 cm-1). The optimum treatment efficiency was studied from 30 CCD conditions in the presence of coolant oil (5%, COD ~ 132,000 mg/L), pH (9), air flow rate (2 L/min), and MIL-88A (1 g) within 177 min. The results obtained from the experiment and the COD prediction were found to be 92.64% and 93.45%, respectively. The main mechanism of iron(III) in MIL-88A is proposed to be the production of hydroxyl radical (·OH) that oxidizes the organic matter in the coolant oil. Moreover, the MAF process was applied to the used industrial coolant oil and was found to be 62.59% efficient.

Discovering the Solid-State Secrets of Lorlatinib by NMR Crystallography: To Hydrogen Bond or not to Hydrogen Bond

Lorlatinib is an active pharmaceutical ingredient (API) used in the treatment of lung cancer. Here, an NMR crystallography analysis is presented whereby the single-crystal X-ray diffraction structure (CSD: 2205098) determination is complemented by multinuclear (1H, 13C, 14/15N, 19F) magic-angle spinning (MAS) solid-state NMR and gauge-including projector augmented wave (GIPAW) calculation of NMR chemical shifts. Lorlatinib crystallises in the P21 space group, with two distinct molecules in the asymmetric unit cell, Z' = 2. Three of the four NH2 hydrogen atoms form intermolecular hydrogen bonds, N30-H…N15 between the two distinct molecules and N30-H…O2 between two equivalent molecules. This is reflected in one of the NH21H chemical shifts being significantly lower, 4.0 ppm compared to 7.0 ppm. Two-dimensional 1H-13C, 14N-1H and 1H (double-quantum, DQ)-1H (single-quantum, SQ) MAS NMR spectra are presented. The 1H resonances are assigned and specific HH proximities corresponding to the observed DQ peaks are identified. The resolution enhancement at a 1H Larmor frequency of 1 GHz as compared to 500 or 600 MHz is demonstrated.

Comparison of methods for 14N-1H recoupling in 14N-1H HMQC MAS NMR

¹H-detected ¹⁴N heteronuclear multiple-quantum coherence (HMQC) magic-angle-spinning (MAS) NMR experiments performed at fast magic-angle spinning (≥50 kHz) are finding increasing application, e.g., to pharmaceuticals. Of importance to the efficacy of these techniques is the recoupling technique applied to reintroduce the ¹H-¹⁴N dipolar coupling. In this paper, we compare, by experiment and 2-spin density matrix simulations, two classes of recoupling scheme: first, those based on n = 2 rotary resonance, namely R³ and spin-polarisation inversion SPI-R³, and the symmetry based SR4₁² method and, second, the TRAPDOR method. Both classes require optimisation depending on the magnitude of the quadrupolar interaction, and thus there is a compromise choice for samples with more than one nitrogen site, as is the case for the studied dipeptide β-AspAla that contains two nitrogen sites with a small and large quadrupolar coupling constant. Considering this, we observe better sensitivity for the TRAPDOR method, though noting the marked sensitivity of TRAPDOR to the ¹⁴N transmitter offset, with both SPI-R³ and SR4₁² giving similar recoupling performance.

Exploring the Potential of Multinuclear Solid-State 1 H, 13 C, and 35 Cl Magnetic Resonance To Characterize Static and Dynamic Disorder in Pharmaceutical Hydrochlorides

Crystallographic disorder, whether static or dynamic, can be detrimental to the physical and chemical stability, ease of crystallization and dissolution rate of an active pharmaceutical ingredient. Disorder can result in a loss of manufacturing control leading to batch-to-batch variability and can lengthen the process of structural characterization. The range of NMR active nuclei makes solid-state NMR a unique technique for gaining nucleus-specific information about crystallographic disorder. Here, we explore the use of high-field ³⁵ Cl solid-state NMR at 23.5 T to characterize both static and dynamic crystallographic disorder: specifically, dynamic disorder occurring in duloxetine hydrochloride (1), static disorder in promethazine hydrochloride (2), and trifluoperazine dihydrochloride (3). In all structures, the presence of crystallographic disorder was confirmed by ¹³ C cross-polarization magic-angle spinning (CPMAS) NMR and supported by GIPAW-DFT calculations, and in the case of 3, ¹ H solid-state NMR provided additional confirmation. Applying ³⁵ Cl solid-state NMR to these compounds, we show that higher magnetic fields are beneficial for resolving the crystallographic disorder in 1 and 3, while broad spectral features were observed in 2 even at higher fields. Combining the data obtained from ¹ H, ¹³ C, and ³⁵ Cl NMR, we show that 3 exhibits a unique case of disorder involving the ⁺ N-H hydrogen positions of the piperazinium ring, driving the chloride anions to occupy three distinct sites.

New salts of teriflunomide (TFM) - Single crystal X-ray and solid state NMR investigation

New salts of teriflunomide TFM (drug approved for Multiple Sclerosis treatment) with inorganic counterions: lithium (TFM_Li), sodium (TFM_Na), potassium (TFM_K), rubidium (TFM_Rb), caesium (TFM_Cs) and ammonium (TFM_NH₄) were prepared and investigated employing solid state NMR Spectroscopy, Powder X-ray Diffraction PXRD and Single Crystal X-ray Diffraction (SC XRD). Crystal and molecular structures of three salts: TFM_Na (CCDC: 2173257), TFM_Cs (CCDC: 2165288) and TFM_NH₄ (CCDC: 2165281) were determined and deposited. Compared to the native TFM, for all crystalline salt structures, a conformational change of the teriflunomide molecule involving about 180-degree rotation of the end group, forming an intramolecular hydrogen bond N-H⋯O is observed. By applying a complementary multi-technique approach, employing 1D and 2D solid state MAS NMR techniques, single and powder X-ray diffraction measurements, as well as the DFT-based GIPAW calculations of NMR chemical shifts for TFM_Na and TFM_Cs allowed to propose structural features of TFM_Li for which it was not possible to obtain adequate material for single crystal X-Ray measurement.

Optimisation of 1H PMLG homonuclear decoupling at 60 kHz MAS to enable 15N-1H through-bond heteronuclear correlation solid-state NMR spectroscopy

The Lee-Goldburg condition for homonuclear decoupling in 1H magic-angle spinning (MAS) solid-state NMR sets the angle θ, corresponding to arctan of the ratio of the rf nutation frequency, ν1, to the rf offset, to be the magic angle, θm, equal to tan-1(√2) = 54.7°. At 60 kHz MAS, we report enhanced decoupling compared to MAS alone in a 1H spectrum of 15N-glycine with at θ = 30° for a ν1 of ∼100 kHz at a 1H Larmor frequency, ν0, of 500 MHz and 1 GHz, corresponding to a high chemical shift scaling factor (λCS) of 0.82. At 1 GHz, we also demonstrate enhanced decoupling compared to 60 kHz MAS alone for a lower ν1 of 51 kHz, i.e., a case where the nutation frequency is less than the MAS frequency, with θ = 18°, λCS = 0.92. The ratio of the rotor period to the decoupling cycle time, Ψ = τr/τc, is in the range 0.53 to 0.61. Windowed decoupling using the optimised parameters for a ν1 of ∼100 kHz also gives good performance in a 1H spin-echo experiment, enabling implementation in a 1H-detected 15N-1H cross polarisation (CP)-refocused INEPT heteronuclear correlation NMR experiment. Specifically, initial 15N transverse magnetisation as generated by 1H-15N CP is transferred back to 1H using a refocused INEPT pulse sequence employing windowed 1H decoupling. Such an approach ensures the observation of through-bond N-H connectivities. For 15N-glycine, while the CP-refocused INEPT experiment has a lower sensitivity (∼50%) as compared to a double CP experiment (with a 200 μs 15N to 1H CP contact time), there is selectivity for the directly bonded NH3+ moiety, while intensity is observed for the CH21H resonances in the double CP experiment. Two-dimensional 15N-1H correlation MAS NMR spectra are presented for the dipeptide β-AspAla and the pharmaceutical cimetidine at 60 kHz MAS, both at natural isotopic abundance. For the dipeptide β-AspAla, different build-up dependence on the first spin-echo duration is observed for the NH and NH3+ moieties demonstrating that the experiment could be used to distinguish resonances for different NHx groups.

Ambiguous structure determination from powder data: four different structural models of 4,11-di-fluoro-quinacridone with similar X-ray powder patterns, fit to the PDF, SSNMR and DFT-D

Four different structural models, which all fit the same X-ray powder pattern, were obtained in the structure determination of 4,11-di-fluoro-quinacridone (C20H10N2O2F2) from unindexed X-ray powder data by a global fit. The models differ in their lattice parameters, space groups, Z, Z', molecular packing and hydrogen bond patterns. The molecules form a criss-cross pattern in models A and B, a layer structure built from chains in model C and a criss-cross arrangement of dimers in model D. Nevertheless, all models give a good Rietveld fit to the experimental powder pattern with acceptable R-values. All molecular geometries are reliable, except for model D, which is slightly distorted. All structures are crystallochemically plausible, concerning density, hydrogen bonds, intermolecular distances etc. All models passed the checkCIF test without major problems; only in model A a missed symmetry was detected. All structures could have probably been published, although 3 of the 4 structures were wrong. The investigation, which of the four structures is actually the correct one, was challenging. Six methods were used: (1) Rietveld refinements, (2) fit of the crystal structures to the pair distribution function (PDF) including the refinement of lattice parameters and atomic coordinates, (3) evaluation of the colour, (4) lattice-energy minimizations with force fields, (5) lattice-energy minimizations by two dispersion-corrected density functional theory methods, and (6) multinuclear CPMAS solid-state NMR spectroscopy (1H, 13C, 19F) including the comparison of calculated and experimental chemical shifts. All in all, model B (perhaps with some disorder) can probably be considered to be the correct one. This work shows that a structure determination from limited-quality powder data may result in totally different structural models, which all may be correct or wrong, even if they are chemically sensible and give a good Rietveld refinement. Additionally, the work is an excellent example that the refinement of an organic crystal structure can be successfully performed by a fit to the PDF, and the combination of computed and experimental solid-state NMR chemical shifts can provide further information for the selection of the most reliable structure among several possibilities.

Separating an overlapped 1H peak and identifying its 1H-1H correlations with the use of single-channel 1H solid-state NMR at fast MAS

Fast magic-angle spinning (≥60 ​kHz) technique has enabled the acquisition of high-resolution ¹H NMR spectra of solid materials. However, the spectral interpretation is still difficult because the ¹H peaks are overlapped due to the narrow chemical shift range and broad linewidths. An additional ¹³C or ¹⁴N or ¹H dimension possibly addresses the issues of overlapped proton resonances, but it leads to the elongated experimental time. Herein, we introduce a single-channel ¹H experiment to separate the overlapped ¹H peak and identify its spatially proximal ¹H-¹H correlations. This sequence combines selective excitation, selective ¹H-¹H polarization transfer by selective recoupling of protons (SERP), and broadband ¹H recoupling by back-to-back (BABA) recoupling sequences. The concept for ¹H separation is based on (i) the selective excitation of a well-resolved ¹H peak and (ii) the selective dipolar polarization transfer from this isolated ¹H peak to one of the ¹H peaks in the overlapped/poor resolution region by SERP and (iii) the detection of ¹H-¹H correlations from these two ¹H peaks to other neighboring ¹Hs by BABA. We demonstrated the applicability of this approach to identify overlapped peaks on two molecules, β-L-aspartyl-l-alanine and Pioglitazone.HCl. The sequence allows the clear observation of ¹H-¹H correlations from an overlapped ¹H peak without an additional heteronuclear dimension and ensures efficient polarization transfers that leads to twelve fold reduction in experimental time compared to ¹⁴N edited experiments. The limitation and the conditions of applicability for this approach are discussed in detail.

Synergy of Solid-State NMR, Single-Crystal X-ray Diffraction, and Crystal Structure Prediction Methods: A Case Study of Teriflunomide (TFM)

In this work, for the first time, we present the X-ray diffraction crystal structure and spectral properties of a new, room-temperature polymorph of teriflunomide (TFM), CSD code 1969989. As revealed by DSC, the low-temperature TFM polymorph recently reported by Gunnam et al. undergoes a reversible thermal transition at -40 °C. This reversible process is related to a change in Z' value, from 2 to 1, as observed by variable-temperature ¹H-¹³C cross-polarization (CP) magic-angle spinning (MAS) solid-state NMR, while the crystallographic system is preserved (triclinic). Two-dimensional ¹³C-¹H and ¹H-¹H double-quantum MAS NMR spectra are consistent with the new room-temperature structure, including comparison with GIPAW (gauge-including projector augmented waves) calculated NMR chemical shifts. A crystal structure prediction procedure found both experimental teriflunomide polymorphs in the energetic global minimum region. Differences between the polymorphs are seen for the torsional angle describing the orientation of the phenyl ring relative to the planarity of the TFM molecule. In the low-temperature structure, there are two torsion angles of 4.5 and 31.9° for the two Z' = 2 molecules, while in the room-temperature structure, there is disorder that is modeled with ∼50% occupancy between torsion angles of -7.8 and 28.6°. These observations are consistent with a broad energy minimum as revealed by DFT calculations. PISEMA solid-state NMR experiments show a reduction in the C-H dipolar coupling in comparison to the static limit for the aromatic CH moieties of 75% and 51% at 20 and 40 °C, respectively, that is indicative of ring flips at the higher temperature. Our study shows the power of combining experiments, namely DSC, X-ray diffraction, and MAS NMR, with DFT calculations and CSP to probe and understand the solid-state landscape, and in particular the role of dynamics, for pharmaceutical molecules.

5-amino-2-methylpyridinium hydrogen fumarate: An XRD and NMR crystallography analysis

Single-crystal X-ray diffraction structures of the 5-amino-2-methylpyridinium hydrogen fumarate salt have been solved at 150 and 300 K (CCDC 1952142 and 1952143). A base-acid-base-acid ring is formed through pyridinium-carboxylate and amine-carboxylate hydrogen bonds that hold together chains formed from hydrogen-bonded hydrogen fumarate ions. ¹ H and ¹³ C chemical shifts as well as ¹⁴ N shifts that additionally depend on the quadrupolar interaction are determined by experimental magic angle spinning (MAS) solid-state nuclear magnetic resonance (NMR) and gauge-including projector-augmented wave (GIPAW) calculation. Two-dimensional homonuclear ¹ H-¹ H double-quantum (DQ) MAS and heteronuclear ¹ H-¹³ C and ¹⁴ N-¹ H spectra are presented. Only small differences of up to 0.1 and 0.6 ppm for ¹ H and ¹³ C are observed between GIPAW calculations starting with the two structures solved at 150 and 300 K (after geometry optimisation of atomic positions, but not unit cell parameters). A comparison of GIPAW-calculated ¹ H chemical shifts for isolated molecules and the full crystal structures is indicative of hydrogen bonding strength.

Investigating discrepancies between experimental solid-state NMR and GIPAW calculation: NC-N 13C and OH⋯O 1H chemical shifts in pyridinium fumarates and their cocrystals

An NMR crystallography analysis is presented for four solid-state structures of pyridine fumarates and their cocrystals, using crystal structures deposited in the Cambridge Crystallographic Data Centre, CCDC. Experimental one-dimensional one-pulse ¹H and ¹³C cross-polarisation (CP) magic-angle spinning (MAS) nuclear magnetic resonance (NMR) and two-dimensional ¹⁴N-¹H heteronuclear multiple-quantum coherence MAS NMR spectra are compared with gauge-including projector augmented wave (GIPAW) calculations of the ¹H and ¹³C chemical shifts and the ¹⁴N shifts that additionally depend on the quadrupolar interaction. Considering the high ppm (>10 ​ppm) ¹H resonances, while there is good agreement (within 0.4 ​ppm) between experiment and GIPAW calculation for the hydrogen-bonded NH moieties, the hydrogen-bonded fumaric acid OH resonances are 1.2-1.9 ​ppm higher in GIPAW calculation as compared to experiment. For the cocrystals of a salt and a salt formed by 2-amino-5-methylpyridinium and 2-amino-6-methylpyridinium ions, a large discrepancy of 4.2 and 5.9 ​ppm between experiment and GIPAW calculation is observed for the quaternary ring carbon ¹³C resonance that is directly bonded to two nitrogens (in the ring and in the amino group). By comparison, there is excellent agreement (within 0.2 ​ppm) for the quaternary ring carbon ¹³C resonance directly bonded to the ring nitrogen for the salt and cocrystal of a salt formed by 2,6-lutidinium and 2,5-lutidinium, respectively.