Conformational Search Research Articles

GIAO NMR Calculation-Driven Stereochemical Assignment of Marine Macrolide Natural Products: Assessment of the Performance of DP4 and DP4+ Analyses and Assignment of the Relative Configuration of Leptolyngbyalide A–C/Oscillariolide Macrolactone

Abstract The stereochemical assignment of marine macrolide natural products by quantum chemical calculations is often hampered by the generation of an intractable number of conformers in molecular mechanics conformation searches. In this study, we assessed in detail the application of GIAO NMR chemical shift calculation and DP4-type statistical analyses to the stereochemical assignment of two marine macrolide natural products, whose relative configurations had been incorrectly assigned in the originally proposed structures. We also examined how DP4+ probability was affected by cumulative Boltzmann population level of molecular mechanics-derived conformers. Finally, GIAO NMR chemical shift calculation/DP4-type statistical analysis was applied to leptolyngbyalide A–C/oscillariolide macrolactone, whose relative configuration has not been assigned so far.

May the Force (Field) Be with You: On the Importance of Conformational Searches in the Prediction of NMR Chemical Shifts.

NMR data prediction is increasingly important in structure elucidation. The impact of force field selection was assessed, along with geometry and energy cutoffs. Based on the conclusions, we propose a new approach named mix-J-DP4, which provides a remarkable increase in the confidence level of complex stereochemical assignments-100% in our molecular test set-with a very modest increment in computational cost.

Computational Studies on Selected Macrolides Active against Escherichia coli Combined with the NMR Study of Tylosin A in Deuterated Chloroform.

Although many antibiotics are active against Gram-positive bacteria, fewer also show activity against Gram-negative bacteria. Here, we present a combination of in silico (electron ion-interaction potential, molecular docking, ADMET), NMR, and microbiological investigations of selected macrolides (14-membered, 15-membered, and 16-membered), aiming to discover the pattern of design for macrolides active against Gram-negative bacteria. Although the conformational studies of 14-membered and 15-membered macrolides are abundant in the literature, 16-membered macrolides, and their most prominent representative tylosin A, have received relatively little research attention. We therefore report the complete 1H and 13C NMR assignment of tylosin A in deuterated chloroform, as well as its 3D solution structure determined through molecular modelling (conformational search) and 2D ROESY NMR. Additionally, due to the degradation of tylosin A in deuterated chloroform, other species were also detected in 1D and 2D NMR spectra. We additionally studied the anti-bacterial activity of tylosin A and B against selected Gram-positive and Gram-negative bacteria.

Theoretical perspective for the relationship between molecular structures and circularly polarised thermally activated delayed fluorescence properties

Circularly polarised thermally activated delayed fluorescence (CP-TADF) molecules producing circularly polarised light which is beneficial to human eyes are widely used in circularly polarised organic light-emitting diodes. However, the relationship between the molecular structures and their luminescence properties of these CP-TADF molecules has not been well explained. Herein, the chiral molecule (R)-SFST with properties of circularly polarised luminescence (CPL) and thermally activated delayed fluorescence (TADF) is studied in detail. Firstly, we found two conformations by using molecular dynamic conformation search for (R)-SFST, namely (R)-SFST-a and (R)-SFST-b. The molecular geometric structures of singlet and triplet states are optimised by utilising density functional theory (DFT) and time-dependent density functional theory (TD-DFT) methods. Combining the thermal vibration correlation function methods, their photophysical properties are studied simultaneously. The processes of excited-state energy decay are revealed. The results show that the chiral units are more important to the molecular orbitals when the molecule has a more distorted configuration, which is beneficial to obtain CPL properties. However, when the molecular has rigid configuration, the excitons are easier to convert between S1 and T1, and the molecular has better TADF properties. Our results reveal the influence of different molecular conformations on CPL and TADF properties.

A coarse-grained approach to NMR-data-assisted modeling of protein structures.

The ESCASA algorithm for analytical estimation of proton positions from coarse-grained geometry developed in our recent work has been implemented in modeling protein structures with the highly coarse-grained UNRES model of polypeptide chains (two sites per residue) and nuclear magnetic resonance (NMR) data. A penalty function with the shape of intersecting gorges was applied to treat ambiguous distance restraints, which automatically selects consistent restraints. Hamiltonian replica exchange molecular dynamics was used to carry out the conformational search. The method was tested with both unambiguous and ambiguous restraints producing good-quality models with GDT_TS from 7.4units higher to 14.4units lower than those obtained with the CYANA or MELD software for protein-structure determination from NMR data at the all-atom resolution. The method can thus be applied in modeling the structures of flexible proteins, for which extensive conformational search enabled by coarse-graining is more important than high modeling accuracy.

Conformational Preference of Flavonols and Its Effect on the Chemical Properties Involved in Radical Scavenging Activity

Flavonols are compounds with radical-scavenging activities that can prevent the harmful effects of free radicals. Their radical-scavenging activity has attracted significant attention. Recently, quantum chemistry-based methodologies have significantly improved the understanding of the activity due to dramatic increases in computational power and software improvements. A standardized analysis method for estimating radical scavenging activity, the quantum mechanics-based test for overall free radical scavenging activity (QM-ORSA), has been proposed. An obstacle in applying the QM-ORSA protocol to flavonols is the large number of conformers and hydroxy groups for analysis. In this study, we focused on it and analyzed the conformational dependences of three flavonols (myricetin, quercetin, and kaempferol) on their chemical properties: bond dissociation energy, pKa, and ionization energy. As a result, all chemical properties were insensitive to conformational differences. The conformational search should be performed separately for each in the gas phase and in aqueous solution because of the differences in the major conformer (relative population of each conformer). These results suggest that it is important to perform the conformational search separately in water and in the gas phase and to determine one representative structure for analyzing radical scavenging activity.

Non-physical Species in Chemical Kinetic Models: A Case Study of Diazenyl Hydroxy and Diazenyl Peroxide.

Predictive chemical kinetic models often consider hundreds to thousands of intermediate species. An even greater number of species are required to generate pressure-dependent reaction networks for gas-phase systems. As this immense chemical search space is being explored using automated tools by applying reaction templates, it is probable that non-physical species will infiltrate the model without being recognized by the compute or a human as such. These non-physical species might obey chemical intuition as well as requirements coded in the software, e. g., obeying element electron valence constraints, and may consequently remain unnoticed. Non-physical species become an acute problem when their presence affects a model observable. Correcting a pressure-dependent network containing a non-physical species may significantly affect the computed rate coefficient. The present work discusses and analyzes two specific cases of such species, diazenyl hydroxy (⋅N=NOH) and diazenyl peroxide (⋅N=NOOH), both previously suggested as intermediates in nitrogen combustion systems. A comprehensive conformational search did not identify any non-fragmented energy well, and energy scans performed for diazenyl peroxide (⋅N=NOOH), at DFT and CCSD(T) show that it barrierlessly decomposes. This work highlights a broad implication for future automated chemical kinetic model generation, and provides a significant motivation to standardize non-physical species identification in chemical kinetic models.

Application of Multiple Length Cross-linkers to the Characterization of Gaseous Protein Structure.

The speed, sensitivity, and tolerance of heterogeneity, as well as the kinetic trapping of solution-like states during electrospray, make native mass spectrometry an attractive method to study protein structure. Increases in the resolution of ion mobility measurements and in mass resolving power and range are leading to the increase of the information content of intact protein measurements and an expanded role of mass spectrometry in structural biology. Herein, a suite of different length noncovalent (sulfonate to positively charged side chain) cross-linkers was introduced via gas-phase ion/ion chemistry and used to determine distance restraints of kinetically trapped gas-phase structures of native-like cytochrome c ions. Electron capture dissociation allowed for the identification of cross-linked sites. Different length linkers resulted in distinct pairs of side chains being linked, supporting the ability of gas-phase cross-linking to be structurally specific. The gas-phase lengths of the cross-linkers were determined by conformational searches and density functional theory, allowing for the interpretation of the cross-links as distance restraints. These distance restraints were used to model gas-phase structures with molecular dynamics simulations, revealing a mixture of structures with similar overall shape/size but distinct features, thereby illustrating the kinetic trapping of multiple native-like solution structures in the gas phase.

Precyclization Conformer Profiles of -SiR3+- and -Bcat+-Activated Linear Si-Protected Hexitols Explain Condensative Cyclization Selectivities.

The condensative cyclization of sp3 C-O bonds in per-silylated hexitols is investigated by computation. Conformer searches using the Monte Carlo algorithm, followed by successively higher levels of theory (MMFF, PM3, and B3LYP), of -SiR3+- and -Bcat+-activated substrates lead to structures primed for intramolecular chemistry. Silane activation features O4 to C1 attack, while borane activation suggests boronium ions that activate O5 to C2 reactivity. This, in conjunction with Boltzmann population analysis, parallels reported reactivity for sorbitol, mannitol, and galactitol. Calculations using the meta-hybrid M06-2X functional additionally provide free-energy profiles for each cyclization event. In most of the cases presented, precyclization conformers that position a nucleophilic oxygen less than 3.0 Å from the C-O leaving group correlate to efficient experimental reactivities. Two examples of galactitol containing bridging silyl groups are analyzed computationally, and the experimental outcomes match predictions. The computational regime presented is a step closer to providing predictive power for the reduction of per-functionalized molecules.

Interaction mechanism of cholesterol/β-cyclodextrin complexation by combined experimental and computational approaches

It is crucial to accurately describe non-covalent weak interactions between the components of cholesterol/β-cyclodextrin inclusion complex in the modulation of its stability. Experimental and theoretical infrared spectra confirmed that the inclusion complex was successfully prepared. Phase solubility studies suggested the formation of 1:1 stoichiometric inclusion complex of cholesterol with β-CD. The inclusion complex showed higher decomposed temperature (327.3 °C) than physical mixture (321.6 °C), indicating improved thermal stability of inclusion complex. Conformational search and density functional theory calculations were performed to find the most stable conformation with the lowest complexation energy (−129.66 kJ/mol). Dispersion energy from van der Waals (−283.31 kJ/mol) contributed greatly on total bonding energy (−204.72 kJ/mol). The bond lengths of hydrogen bonds (O127⋅⋅⋅H221 and O220⋅⋅⋅H107) were 1.77 and 1.62 Å, respectively. Van der Waals and hydrogen bonds were necessary to drive spontaneous formation and maintain the stability of inclusion complex. This study revealed a deep insight into the formation mechanism of cholesterol/β-CD inclusion complex using computational and experimental approaches, providing theoretical basis for the removal of cholesterol from hydrocolloid-containing systems. • Mechanism of β-CD complexation with cholesterol was illustrated through experimental and computational methods. • The thermal stability of cholesterol/β-CD inclusion complex was significantly improved. • Weak interactions of the complex were shown by means of images and data. • The inclusion complex was mainly stabilized by hydrogen bonds and van der Waals forces.

Unbiased disentanglement of conformational baths with the help of microwave spectroscopy, quantum chemistry, and artificial intelligence: The puzzling case of homocysteine.

An integrated experimental-computational strategy for the accurate characterization of the conformational landscape of flexible biomolecule building blocks is proposed. This is based on the combination of rotational spectroscopy with quantum-chemical computations guided by artificial intelligence tools. The first step of the strategy is the conformer search and relative stability evaluation performed by means of an evolutionary algorithm. In this step, last generation semiempirical methods are exploited together with hybrid and double-hybrid density functionals. Next, the barriers ruling the interconversion between the low-lying conformers are evaluated in order to unravel the possible fast relaxation paths. The relative stabilities and spectroscopic parameters of the "surviving" conformers are then refined using state-of-the-art composite schemes. The reliability of the computational procedure is further improved by the inclusion of vibrational and thermal effects. The final step of the strategy is the comparison between experiment and theory without any ad hoc adjustment, which allows an unbiased assignment of the spectroscopic features in terms of different conformers and their spectroscopic parameters. The proposed approach has been tested and validated for homocysteine, a highly flexible non-proteinogenic α-amino acid. The synergism of the integrated strategy allowed for the characterization of five conformers stabilized by bifurcated N-H2⋯O=C hydrogen bonds, together with an additional conformer involving a more conventional HN⋯H-O hydrogen bond. The stability order estimated from the experimental intensities as well as the number and type of conformers observed in the gas phase are in full agreement with the theoretical predictions. Analogously, a good match has been found for the spectroscopic parameters.

INTERFACES. A program for determining the 3D structures of surfaces sites using NMR data

Dynamic nuclear polarization surface enhanced NMR spectroscopy has enabled the determination of high-resolution structures from surface-supported molecules, including single-site heterogeneous catalysts. Structure determinations have largely mimicked the approaches used in biomolecular NMR spectroscopy, namely, using distance measurements to constrain a conformational search. These early demonstrations made use of purpose-built software, which has limited the adoption of the technique. Herein, we describe the open-source program INTERFACES (Interpret NMR to Elucidate or Reconstruct the Full Atomistic Configurations of External Surfaces) which automates the analysis of RE(SP)DOR data as well as the structure determination for surface sites. Distances, angles, dihedral angles, complex orientation, and distance from the support can all be sampled to find all structures that agree with the experimental data. A χ2 metric is used to define the error ranges of the REDOR fits and produce structures with an arbitrary level of confidence. Structural solutions are then provided as both overlays and ORTEP-like probability ellipsoids.

Narrowing down the conformational space with solid-state NMR in crystal structure prediction of linezolid cocrystals

Many solids crystallize as microcrystalline powders, thus precluding the application of single crystal X-Ray diffraction in structural elucidation. In such cases, a joint use of high-resolution solid-state NMR and crystal structure prediction (CSP) calculations can be successful. However, for molecules showing significant conformational freedom, the CSP-NMR protocol can meet serious obstacles, including ambiguities in NMR signal assignment and too wide conformational search space to be covered by computational methods in reasonable time. Here, we demonstrate a possible way of avoiding these obstacles and making as much use of the two methods as possible in difficult circumstances. In a simple case, our experiments led to crystal structure elucidation of a cocrystal of linezolid (LIN), a wide-range antibiotic, with 2,3-dihydroxybenzoic acid, while a significantly more challenging case of a cocrystal of LIN with 2,4-dihydroxybenzoic acid led to the identification of the most probable conformations of LIN inside the crystal. Having four rotatable bonds, some of which can assume many discreet values, LIN molecule poses a challenge in establishing its conformation in a solid phase. In our work, a set of 27 conformations were used in CSP calculations to yield model crystal structures to be examined against experimental solid-state NMR data, leading to a reliable identification of the most probable molecular arrangements.

Exploring Conformational Preferences of Leu-enkephalin Using the Conformational Search and Double-Hybrid DFT Energy Calculations.

The conformational preferences of Leu-enkephalin (Leu-Enk) were explored by the conformational search and density functional theory (DFT) calculations. By a combination of low-energy conformers of each residue, the initial structures of the neutral Leu-Enk were generated and optimized using the ECEPP3 force field in the gas phase. These structures were reoptimized at the HF/3-21G(d) and M06-2X levels of theory with 6-31G(d) and 6-31+G(d) basis functions. We finally located the 139 structures with the relative energy <10 kcal mol–1 in the gas phase, from which the structures of the corresponding zwitterionic Leu-Enk were generated and reoptimized at the M06-2X/6-31+G(d) level of theory using the implicit solvation model based on density (SMD) in water. The conformational preferences of Leu-Enk were analyzed using Gibbs free energies corrected by single-point energies calculated at the double-hybrid DSD-PBEP86-D3BJ/def2-TZVP level of theory in the gas phase and in water. The neutral Leu-Enk dominantly adopted a folded structure in the gas phase stabilized by three H-bonds with a βII′-bend-like motif at the Gly3–Phe4 sequence and a close contact between the side chains of Phe4 and Leu5. The zwitterionic Leu-Enk exhibited a folded structure in water stabilized by three H-bonds with double β-bends such as a βII′ bend at the Gly2–Gly3 sequence and a βI bend at the Gly3–Phe4 sequence. The calculated ensemble-averaged distance between CGly2α and CLeu5α of the zwitterionic Leu-Enk in water is consistent with the value estimated from the simulated annealing using the distance constraints derived from nuclear Overhauser effect spectroscopy (NOESY) spectra in water. Interestingly, the preferred conformations of the neutral and zwitterionic Leu-Enk are new folded structures not predicted by earlier computational studies. According to the refined model of the zwitterionic Leu-Enk bound to δ-opioid receptor (δOR), there were favorable interactions of the terminal charged groups of Leu-Enk with the side chains of charged residues of δOR as well as a favorable CAryl···H interaction of the Phe4 residue of Leu-Enk with Trp284 of δOR. Hence, these favorable interactions would induce the folded structure of the zwitterionic Leu-Enk with double β-bends isolated in water into the “bioactive conformation” like an extended structure when binding to δOR.

A spectroscopic approach to identifying the out-of-plane conformations of Ni(II) meso-tetraphenylporphyrin in solution

Ni(II) meso-tetraphenylporphyrin (NiTPP) is a model molecule whose substituent causes out-of-plane (oop) deformations of the porphyrin macrocycle. Although the conformers of NiTPP in the solution had been tentatively explored, the determination of its specific conformers was controversial. In this work, based on the conformational search through molecular dynamics (MD), three energy lowest-lying conformers of NiTPP were sorted out, namely, the S4 (staggered) conformer, the C2 (eclipsed) conformer, and the C1 (eclipsed-staggered) conformer. According to the high-precision free energy calculation based on density functional theory (DFT), the Raman and 1H-NMR spectra of the three conformers were calculated. The actual spectra of NiTPP in solution resulted from the sum spectra of the mixture conformers, so with the consideration of the corresponding conformation weights, the experimental spectra could be stimulated. Our results showed that only at the low-frequency ∼215 cm−1, did the Raman spectrum in solution differ significantly from that in solid powder. On the other hand, the 1H-NMR spectra of the NiTPP conformers were remarkably different, and none of the single conformer's 1H-NMR range could match the experimental 1H-NMR spectrum. However, with the consideration of the existence of three dominant conformations, the observed 1H-NMR spectrum could be well simulated, confirming the rational mixture of the three dominant conformers existing in the aqueous solution. Therefore, this work has not only resolved the different conformers of NiTPP in solution, but also provided an effective approach to combining DFT, Raman, and 1H-NMR analytical tools for identifying different oop conformations of metalloporphyrins in solution.

Mebendazole's Conformational Space and Its Predicted Binding to Human Heat-Shock Protein 90.

Recent experimental evidence suggests that mebendazole, a popular antiparasitic drug, binds to heat shock protein 90 (Hsp90) and inhibits acute myeloid leukemia cell growth. In this study we use quantum mechanics (QM), molecular similarity, and molecular dynamics (MD) calculations to predict possible binding poses of mebendazole to the adenosine triphosphate (ATP) binding site of Hsp90. Extensive conformational searches and minimization of the five mebendazole tautomers using the MP2/aug-cc-pVTZ theory level resulted in 152 minima. Mebendazole-Hsp90 complex models were subsequently created using the QM optimized conformations and protein coordinates obtained from experimental crystal structures that were chosen through similarity calculations. Nine different poses were identified from a total of 600 ns of explicit solvent, all-atom MD simulations using two different force fields. All simulations support the hypothesis that mebendazole is able to bind to the ATP binding site of Hsp90.

Analysis of the sidechain structures of amino acids and peptides and a deduced method for the efficient search of peptide conformations

To reduce the dimensionality of the potential energy surface (PES) necessary for finding the low energy conformations (LECs) of peptides, the sidechain dihedral angles (DAs) of 3548 LECs of 17 amino acids (AAs) and related peptides are examined. The analysis reveals that most DAs can be discretized into 3 states. Moreover, the fact that many DA combinations are absent in the LECs is utilized to construct a new conformational search method named as the TM method. For a peptide with N AA residues, the TM method is 1.5N times faster than considering all DA combinations, and 4.7N times faster than the conventional Newman projection method. The reliability of the TM results is confirmed through testing on 11 dipeptides and 2 tetrapeptides. The much reduced PES size of the TM method allows the database building of diverse peptide structures, and enhances the reliability of various stochastic sampling based methods.

Prenol as a Next-Generation Biofuel or Additive: A Comprehension of the Hydrogen Abstraction Reactions by a H Atom.

Thermal rate coefficients for the hydrogen abstraction reactions of prenol (3-methyl-2-butenol) by a hydrogen atom were calculated with the multipath canonical variational theory with small-curvature tunneling (MP-CVT/SCT). The conformational search was performed with a dual-level approach, and the multistructural torsional anharmonicity effects were corrected through the rovibrational partition function calculated with the multistructural method based on a coupled torsional potential (MS-T(C)). This methodology allows us to estimate the thermal rate constants in the temperature range of 200-2500 K and fit them into two analytical expressions. Differences between the number of conformations on the torsional potential energy surfaces for prenol and the transition state decrease the thermal rate constants for the H-abstraction at the α carbon. An opposite behavior was detected for the abstractions on the δ site. The product branching ratios were calculated using single-structure and multipath approaches. The product distributions from the former are shown to be inadequate for studying the mechanism under combustion conditions. The values estimated from MP-CVT/SCT rate coefficients indicated that the radicals from (Rα) and (Rδ)/(Rδ') are formed in considerable amounts. These species are fundamental in comprehending the inhibition and promotion of the autoignition phenomena.

A stacked meta-ensemble for protein inter-residue distance prediction

Predicted inter-residue distances are a key behind recent success in high quality protein structure prediction (PSP). However, prediction of both short and long distance values together is challenging. Consequently, predicted short distances are mostly used by existing PSP methods. In this paper, we use a stacked meta-ensemble method to combine deep learning models trained for different ranges of real-valued distances. On five benchmark sets of proteins, our proposed inter-residue distance prediction method improves mean Local Distance Different Test (LDDT) scores at least by 5% over existing such methods. Moreover, using a real-valued distance based conformational search algorithm, we also show that predicted long distances help obtain significantly better protein conformations than when only predicted short distances are used. Our method is named meta-ensemble for distance prediction (MDP) and its program is available from https://gitlab.com/mahnewton/mdp.

Molecular Conformer Search with Low-Energy Latent Space.

Identifying low-energy conformers with quantum mechanical accuracy for molecules with many degrees of freedom is challenging. In this work, we use the molecular dihedral angles as features and explore the possibility of performing molecular conformer search in a latent space with a generative model named variational auto-encoder (VAE). We bias the VAE towards low-energy molecular configurations to generate more informative data. In this way, we can effectively build a reliable energy model for the low-energy potential energy surface. After the energy model has been built, we extract local-minimum conformations and refine them with structure optimization. We have tested and benchmarked our low-energy latent-space (LOLS) structure search method on organic molecules with 5–9 searching dimensions. Our results agree with previous studies.