Bond Rotation Research Articles

Conformational Analysis and DFT Investigations of 1-(4-Fluorophenyl)Piperazine by ELF and LOL, Inhibitory activity against Alzheimer’s Disease, and ADME Prediction

This study reports 1-(4-Fluorophenyl)Piperazine molecule structural and electronic properties calculated at the DFT/B3LYP level. A potential energy surface scan along the rotational bonds discovered the most stable minimum energy conformer of the title compound. Frontier molecular orbital (FMO) analyses, density of state (DOS), molecular electrostatic potential (MEP), and global and chemical reactivity descriptors were also used to investigate the reactivity of the pFPP molecule. In addition, ELF and LOL analysis were performed. In silico biological studies such as drug-likeness, ADME, and toxicity properties were also performed. Molecular docking studies are performed to predict the anti-Alzheimer agent enzyme (AChE) active site of the pFPP. The docking predicts the possibility of a potential drug to improve Alzheimer's disease (AD) treatment.

Singlet Oxygen's Potential Role as a Nonoxidative Facilitator of Disulfide S-S Bond Rotation†.

The role of singlet oxygen potentially mediating increased conformational flexibility of a disulfide was investigated. Density functional theory (DFT) calculations indicate that the singlet oxygenation of 1,2-dimethyldisulfane produces a peroxy intermediate. This intermediate adopts a structure with a longer S-S bond distance and a more planar torsional angle θ (C-S-S-C) compared with the nonoxygenated 1,2-dimethyldisulfane. The lengthened S-S bond enables a facile rotation about the torsional angle in the semicircle region 0° < θ < 210°, that is ~5 kcal mol-1 lower in energy than the disulfane. The peroxy intermediate bears nO → σS-S and nO → σ*S-S interactions that stabilize the S-O bond but destabilize the S-S bond, which contrasts with stabilizing nS → σ*S-S hyperconjugative effects in the disulfane S-S bond. Subsequent departure of O2 from the disulfane peroxy intermediate is reminiscent of peroxy intermediates which also expel O2 , yet facilitate cis-trans isomerizations of stilbenes, hexadienes, cyanines, and carotenes. "Non-oxidative" 1 O2 interactions with a variety of bond types are currently underappreciated. We hope to raise awareness of how these interactions can help elucidate the origins of molecular twisting.

Activating dislocation mediated plasticity in boron carbide through Al-doping

Dislocation slip, deformation twinning, phase transformations, and fast fracture are energy dissipation mechanisms that accommodate mechanical loading in materials. The energetically unfavorable formation of dislocation attributes to the ease of cracking and the low damage tolerance observed in superhard ceramics, notably boron carbide. This work demonstrates that room temperature dislocation slip can be enabled in boron carbide by altering its chemistry through Al doping. The activation of dislocation slip is mechanistically explained by quantum mechanics simulations and electron microscopy, which indicate that strain energy is released through basal icosahedral slip facilitated by icosahedral rotation and chain bond breaking and reconfiguring. The new insight gained from this work suggests that atomic doping could be an effective strategy to tune deformation mechanisms in boron carbide, which provides a significant potential for limiting amorphization and catastrophic failure, and opens a new strategy to enhance damage tolerance in brittle ceramics.

Revealing and Tuning the Photophysics of C=N Containing Photothermal Molecules: Excited State Dynamics Simulations.

Molecular photothermal conversion materials are recently attracting increasing attention for phototherapy applications. Herein we investigate the excitation and de-excitation processes of a photothermal molecule (C1TI) that is among the recently developed class of small-molecule-based photothermal imines with superb photothermal conversion efficiencies (PTCEs) up to 90% and a molecule (M2) that is constructed by replacing the amino group of C1TI with an H atom, via excited-state dynamics simulations based on the time-dependent density functional theory (TD-DFT). The simulations reveal fast (<150 fs of average time) nonradiative decays of the lowest excited singlet (S1) state to a conical intersection (CI) with the ground (S0) state in high yields (C1TI: 93.9% and M2: 87.1%). The fast decays, driven by C=N bond rotation to a perpendicular structural configuration, are found to be barrierless. The slight structural difference between C1TI and M2 leads to drastically different S0-S1 energy surfaces, especially M2 features a relatively much lower CI (0.8 eV in energy) and much more decay energy (1.0 eV) to approach the CI. This work provides insights into the de-excitation mechanisms and the performance tuning of C=N enabled photothermal materials.

Extended Double Bond Conjugation in the Chalcone Framework Favours MAO-B Inhibition: A Structural Perspective on Molecular Dynamics.

The monotropic membrane protein monoamine oxidase B (MAO-B) has been shown to be a crucial drug target for the treatment of neurodegenerative diseases. The design of recent inhibitor therapeutic agents of MAO-B involves conjugation and modification of a chalcone scaffold comprising two aryl or heteroaryl rings connected via a short spacer unit with rotatable bonds. Supported by experimental data, these modifications often result in high potent inhibitor compounds. In this study, we employ molecular dynamics simulations to unravel the impact of extended double bond conjugation in two novel compounds, F1 and MO10, toward the inhibition of the MAO-B protein. It was revealed that extended double bond conjugation induced a unidirectional orientation and motion of F1 and MO10, suggesting a stable binding pocket anchorage favouring high-affinity pocket interactions. Conformational analyses also revealed that the incorporated double bond extension impeded the motion of individual binding pocket residues, which subsequently disrupted the functionality of MAO-B. Real-time structural dynamics also revealed that the extended double bond conjugation mediated peculiar interactions with MAO-B binding pocket residues characterized by π-alkyl, π-π stacking, and π-sulphur interactions which buried both compounds into the hydrophobic core of MAO-B and ultimately induced higher binding affinities of both F1 and MO10. These insights present useful structural perspectives of the extended double bond conjugation associated with the experimentally reported enhanced inhibitory activity of F1 and MO10 against MAO-B.

Mechanical properties of pristine and nanocrystalline graphene up to ultra-high temperatures

Despite being the basic building block of most carbon materials used in high and ultra-high temperature applications, the mechanical properties of graphene at such temperatures remain totally unknown. Here we compute these properties using tensile molecular dynamics simulations at temperatures ranging from room temperature to 5000 K (i. e. about the melting temperature) for pristine and nanocrystalline graphene. Mechanical simulations at such temperatures are made possible via the use of the screened environment dependent reactive empirical bond order potential [Perriot et al. Phys. Rev. B 88, 064101 (2013)]. We show that even at the highest temperature, both graphene and nanocrystalline graphene retain high stiffness, strength and fracture strain. Analyses of tensile curves and trajectories (including an analysis of in-plane non-affine atomic displacements) show that both pristine and nanocrystalline graphene show brittle rupture, whatever the temperature, even though some early sign of ductility can be detected for the nanocrystalline graphene at 5000 K. This rules out the possibility of a ductile fracture in graphene at any temperature below the melting point. Finally, the simulations also highlight the importance of bond rotation (Stone-Wales) based defects in the fracture initiation mechanism for pristine graphene. Especially at intermediate temperature (3000 K) crack nucleation in pristine graphene is shown to take place exactly at the moment and place of the first Stone-Wales defect formation.

Antisymmetric stretching vibration of sulfur dioxide and carbon disulfide modified by optical cavity

For sulfur dioxide (SO2) and carbon disulfide (CS2) molecules in the optical cavity, we study the collective asymmetric Rabi splitting of vibrational strong coupling (VSC) and vibrational ultrastrong coupling (V-USC) between the antisymmetric stretching vibration mode of SO2/CS2 and the optical cavity mode using molecular dynamics simulations. We also study the modification effects of the optical cavity on their ground state bond lengths and rotation behavior. Through the simulation results, we find that although the asymmetric Rabi splitting phenomenon can both occur for SO2 and CS2 molecules, the promotion (or inhibition) effects on their upper polarons (UPs) are different with the increase of the coupling strength. In addition, we find that the relationship between polaron frequencies of SO2 molecules and cavity mode frequencies is consistent with that of CS2 molecules when the cavity mode frequency is highly positively detuned. However, the lower polaron(LP) of SO2 almost disappears and the LP's characteristic of CS2 is dominated by the cavity mode when the cavity mode frequency is highly negatively detuned. Finally, we find that there are obvious hole effects on the ground state rotation behavior of the two molecules. By comparing the different modification effects of the cavity on ground polar molecules (SO2 molecules) and ground non-polar molecules (CS2 molecules), we can not only further understand the differences between the vibrational modes of SO2 and CS2 molecules, but also provide important evidence that we may be able to change the chemical properties of SO2 and CS2 molecules by using VSC-V-USC in a reversible way. In addition, the cavity mode is used to regulate their UP and LP, which opens up a new way to control the physical and chemical properties of SO2 and CS2 molecules. Meanwhile, it also provides reliable information for vibration-polariton science, and provides comparable results for more complex experiments of light—matter coupling in the future.

Computationally Elucidating the Binding Kinetics for Different AChE Inhibitors to Access the Rationale for Improving the Drug Efficacy.

Traditional drug discovery is based on a binding affinity (thermodynamics)-driven paradigm. Numerous examples, however, demonstrated that drug efficacy does not always depend only on binding affinity but positively correlates with binding kinetics, that is, the dissociation rate constant (koff). Binding free energy landscape (BFEL) constructor is a computational binding kinetics prediction method, previously developed by us, that estimates the binding kinetics for ligand-protein based on their constructed binding free energy landscape, but it also reveals the detailed molecular mechanism of the binding event, hence, providing the position of transition states at the molecular level to modify/improve the binding kinetics. Acetylcholinesterase (AChE) is a well-known Alzheimer's disease (AD) target for which there is still not an ideal drug on the market. Therefore, to improve the drug design strategy for AD, the binding kinetics and binding molecular mechanisms of the four inhibitors of AChE, that is, E2020 (Aricept), HupA, Rivastigmine, and Galantamine, were studied. Also, the differentiation of the binding kinetics between mAChE and TcAChE was studied to evaluate the sensitiveness of BFEL constructor. The flexibility of molecules has a noticeable effect on the nature of BFEL. To the same target, flexible molecules (i.e., E2020 and Rivastigmine) which contain more rotatable bonds tend to have more complicated BFELs reflecting more complicated molecular action mechanisms than the rigid ones (i.e., HupA and Galantamine), which therefore could be more challenging to be optimized. The binding kinetics is highly dependent on the structure of the molecules, such as the length and the functional groups. Therefore, E2020 presents better binding kinetic and thermodynamic properties with either TcAChE or mAChE. Therefore, it is the most promising lead drug for binding kinetics-based drug design. In addition, the binding kinetics of a drug may present different values in the proteins of different organisms because the residue compositions of the binding gorges of the targets are variant, that is, E2020 shows lower binding affinity and association energy barrier in binding with mAChE than TcAChE. However, HupA presents a better binding property with TcAChE than mAChE.

Atropisomerism in the Pharmaceutically Relevant Realm.

ConspectusAtropisomerism is a conformational chirality that occurs when there is hindered rotation about a σ-bond. While atropisomerism is exemplified by biaryls, it is observed in many other pharmaceutically relevant scaffolds including heterobiaryls, benzamides, diarylamines, and anilides. As bond rotation leads to racemization, atropisomers span the gamut of stereochemical stability. LaPlante has classified atropisomers based on their half-life of racemization at 37 °C: class 1 (t1/2 < 60 s), class 2 (60 s < t1/2 < 4.5 years), and class 3 (t1/2 > 4.5 years). In general, class-3 atropisomers are considered to be suitable for drug development. There are currently four FDA-approved drugs that exist as stable atropisomers, and many others are in clinical trials or have recently appeared in the drug discovery literature. Class-1 atropisomers are more prevalent, with ∼30% of recent FDA-approved small molecules possessing at least one class-1 axis. While class-1 atropisomers do not possess the requisite stereochemical stability to meet the classical definition of atropisomerism, they often bind a given target in a specific set of chiral conformations.Over the past decade, our laboratory has embarked on a research program aimed at leveraging atropisomerism as a design feature to improve the target selectivity of promiscuous lead compounds. Our studies initially focused on introducing class-3 atropisomerism into promiscuous kinase inhibitors, resulting in a proof of principle in which the different atropisomers of a compound can have different selectivity profiles with potentially improved target selectivity. This inspired a careful analysis of the binding conformations of diverse ligands bound to different target proteins, resulting in the realization that the sampled dihedral conformations about a prospective atropisomeric axis played a key role in target binding and that preorganizing the prospective atropisomeric axis into a desired target’s preferred conformational range can lead to large gains in target selectivity.As atropisomerism is becoming more prevalent in modern drug discovery, there is an increasing need for strategies for atropisomerically pure samples of pharmaceutical compounds. This has led us and other groups to develop catalytic atroposelective methodologies toward pharmaceutically privileged scaffolds. Our laboratory has contributed examples of atroposelective methodologies toward heterobiaryl systems while also exploring the chirality of less-studied atropisomers such as diarylamines and related scaffolds.This Account will detail recent encounters with atropisomerism in medicinal chemistry and how atropisomerism has transitioned from a “lurking menace” into a leverageable design strategy in order to modulate various properties of biologically active small molecules. This Account will also discuss recent advances in atroposelective synthesis, with a focus on methodologies toward pharmaceutically privileged scaffolds. We predict that a better understanding of the effects of conformational restriction about a prospective atropisomeric axis on target binding will empower chemists to rapidly “program” the selectivity of a lead molecule toward a desired target.

Molecular docking and in vitro experiments verified that kaempferol induced apoptosis and inhibited human HepG2 cell proliferation by targeting BAX, CDK1, and JUN.

Hepatocellular carcinoma, as a common liver cirrhosis complication, has become the sixth most common cancer worldwide, and its increasing incidence has resulted in considerable medical and economic burdens. As a natural polyphenolic compound, kaempferol has exhibits a wide range of antitumor activities against multiple cancer targets. In this study, the Autodock software was used for molecular docking to simulate the interaction process between kaempferol and HCC targets and the PyMOL software was used for visualization. Proliferation of kaempferol HepG2 cells under the effect of kaempferol was detected using Cell Counting Kit-8 (CCK-8) assay, and the apoptosis rate of HepG2 cells was detected using flow cytometry. The expressions of proteins BAX, CDK1, and JUN protein expressions were detected by Western blot. Molecular docking found that the kaempferol ligand has 3 rotatable bonds, 6 nonpolar hydrogen atoms, and 12 aromatic carbon atoms, and can form complexes with the kaempferol targets P53, BAX, AR, CDK1, and JUN through electrostatic energy. GO (Gene Ontology) enrichment analysis suggests that kaempferol regulates the biological function of hepatocellular carcinoma cells and is related to apoptosis. Cell Counting Kit-8 assay suggested that Kaempferol can significantly inhibited HepG2 cell proliferation, and the inhibition rate increased with the increase in drug concentration and incubation time. Moreover, kaempferol can promoted HepG2 cell apoptosis in a dose-dependent manner. This compound upregulated BAX and JUN expression and downregulated CDK1 expression. Thus, Kaempferol can promote HepG2 cell apoptosis, and the regulatory mechanism may be related to the regulation of the expression levels of the apoptosis-related proteins BAX, CDK1, and JUN.

Atropisomerism in Drug Discovery: A Medicinal Chemistry Perspective Inspired by Atropisomeric Class I PI3K Inhibitors.

Atropisomerism is a type of axial chirality resulting from hindered rotation about a σ bond that gives rise to nonsuperimposable stereoisomers (termed "atropisomers"). The inversion of chirality of an atropisomeric axis is a time- and temperature-dependent dynamic process occurring by simple bond rotation. For this reason, the rotational energy barrier (ΔErot) and the interconversion rate between an atropisomeric pair of biologically active molecules are important parameters to consider in drug discovery.Many compounds with atropisomeric axes advance into development every year. The vast majority of them have low rotational energy barriers (ΔErot lower than 20 kcal/mol), meaning they are rapidly equilibrating conformers and considered achiral (class 1 atropisomers). Compounds in class 2 (ΔErot = 20 to 30 kcal/mol) can be challenging to develop given that the stereochemical integrity of the atropisomeric axes can be compromised over time. It has been recommended that small molecule drug candidates containing one or more atropisomeric axes with rotational energy barriers greater than 30 kcal/mol (class 3 atropisomers) should be developed as single atropisomers.In medicinal chemistry, a σ bond with restricted rotation is engineered into a bioactive molecule primarily to limit its number of accessible conformations, thereby minimizing entropic and/or enthalpic energy penalties associated with biological target binding. In addition to enhanced pharmacology, potential positive outcomes of introducing atropisomerism include improved physicochemical properties and superior pharmacokinetics/ADME profiles. The application of atropisomerism in medicinal chemistry has become increasingly enabled due to recent advances in synthesis, purification, and analysis, as described in this special issue and recent review articles.Herein, we discuss two case studies from our own work in which restricting rotation about axes of atropisomerism led to significant improvements in pharmacological, physicochemical, and ADME properties for different series of PI3K inhibitors. In the first instance, a restricted axis of rotation was designed to mitigate an acid-mediated hydrolytic degradation pathway observed in a series of PI3Kδ inhibitors. The conformational constraint disrupts conjugation between a quinazolinone and a pyridine, leading to improved chemical stability under acidic conditions. In the second case study, introduction of a restricted axis of rotation between two heteroaromatic systems in a series of PI3Kβ inhibitors generated pairs of atropisomeric compounds with significantly different biological activities. Advanced profiling also demonstrated clear substrate stereospecificity in regard to metabolism by aldehyde oxidase. Gratifyingly, the eutomer (more active atropisomer) shows significantly less susceptibility for oxidative metabolism relative to the distomer (less active atropisomer). The improvements in potency, selectivity, chemical stability, and metabolic stability discussed in this manuscript are all directly related to the concept of atropisomerism.

Phase-transition kinetics of calcium-doped TiO2: A high-temperature XRD study

Controlling titanium dioxide crystallinity is crucial in view of the possible oxide applications. In this study, we examined the effects of calcium doping on the anatase-rutile phase transition via in-situ high-temperature X-ray diffraction. The phase transition temperature of calcium-doped TiO2 was approximately 900 °C, specifically 900 °C, 875 °C, and 900 °C for the 2%, 4%, and 6% calcium-doped TiO2, respectively. The larger radius of the calcium ion compared to that of the titanium ion hindered the calcium incorporation into the TiO2 lattice. Moreover, the hampered titanium-oxygen bond rotation during the phase transition led to an increase in the phase-transformation temperature. Furthermore, at higher calcium concentrations, the corresponding activation energies increased first and then decreased. This may have been controlled by the decreasing nucleation rate during the reaction.

Insight into Atomic-Scale Adhesion at the C–Cu Interface During the Initial Stage of Nanoindentation

Adhesion is a common phenomenon in nanomachining which affects processing accuracy and repeatability. As material removal approaches the atomic or close-to-atomic scale, quantum mechanics becomes the dominant principle behind the atomic-level interaction. However, atomic-scale effects cannot be properly described by empirical potential function-based molecular dynamics simulations. This study uses a first-principles method to reveal the atomic-scale adhesion between a diamond tip and a copper slab during initial-stage nanoindentation. Using a simplified tip and slab model, adhesion energy, electronic distribution, and density of states are analyzed based on quantum chemistry calculation. Results show that atomic adhesion is primarily due to the covalent bonding interaction between C and Cu atoms, which can induce structural changes to the diamond tip and copper slab. The effects of tip position and angles on adhesion are further studied through a series of simulations. The results show that adhesion between the tip and slab is sensitive to the lattice structure and a variant in angstroms is enough to cause different adhesion and structural changes. The actual determinants of adhesion can only be the atomic and electronic structures at the tip–slab interface. Bond rotation and breakage are observed during simulation and their effects on adhesion are further discussed. To conclude, the first-principles method is important for the analysis of an atomic-scale interaction system, even if only as an aid to describing adhesion at atomic and electronic scales.

Mechanism of saikogenin G against major depressive disorder determined by network pharmacology.

Many classic decoctions of Chinese medicine including Radix Bupleuri are used to treat major depressive disorder (MDD). Saikosaponin D is a representative bioactive ingredient discovered in Radix Bupleuri. The mechanism of saikogenin G (SGG) as a metabolite in MDD remains unclear to date. This study aims to elucidate the mechanism of SGG in treating MDD with network pharmacology.We evaluated the drug likeness of SGG with SwissADME web tool and predicted its targets using the SwissTargetPrediction and PharmMapper. MDD-related targets were identified from the following databases: DisGeNET, DrugBank, Online Mendelian Inheritance in Man, and GeneCards. The common targets of SGG and MDD were imported to the STRING11.0 database, and then a protein–protein interaction network was constructed. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment were analyzed with DAVID 6.8 database.The molecular weight of SGG was 472.7 g/mol, the topological polar surface area was 69.92 A2 <140 A2, the octanol/water partition coefficient (Consensus LogP0/W) was 4.80, the rotatable bond was 1, the hydrogen bond donors was 3, and the hydrogen bond acceptors was 4. A total of 322 targets of SGG were obtained and there were 1724 MDD-related targets. A total of 78 overlapping genes were selected as targets of MDD treatment including albumin, insulin-like growth factor I, mitogen-activated protein kinase 1, proto-oncogene tyrosine-protein kinase Src, and epidermal growth factor receptor. Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis suggested that proteoglycans in cancer, pathways in cancer, prostate cancer, hypoxia-inducible factor-1, central carbon metabolism in cancer, estrogen, PI3K-Akt, ErbB, Rap1, and prolactin signaling pathways played an important role(P < .0001).This study showed that SGG exhibits good drug-like properties and elucidated the potential mechanisms of SGG in treating MDD with regulating inflammation, energy metabolism, monoamine neurotransmitters, neuroplasticity, phosphocreatine-creatine kinase circuits, and so on.

Non-Immunosuppressive Cyclophilin Inhibitors.

Cyclophilins, enzymes with peptidyl-prolyl cis/trans isomerase activity, are relevant to a large variety of biological processes. The most abundant member of this enzyme family, cyclophilin A, is the cellular receptor of the immunosuppressive drug cyclosporine A (CsA). As a consequence of the pathophysiological role of cyclophilins, particularly in viral infections, there is a broad interest in cyclophilin inhibition devoid of immunosuppressive activity. This Review first gives an introduction into the physiological and pathophysiological roles of cyclophilins. The presentation of non-immunosuppressive cyclophilin inhibitors will commence with drugs based on chemical modifications of CsA. The naturally occurring macrocyclic sanglifehrins have become other lead structures for cyclophilin-inhibiting drugs. Finally, de novo designed compounds, whose structures are not derived from or inspired by natural products, will be presented. Relevant synthetic concepts will be discussed, but the focus will also be on biochemical studies, structure-activity relationships, and clinical studies.

Pyridine‐oxazoline ligated iron complexes: Synthesis, characterization, and catalytic activity for isoprene polymerization

A series of iron(II) dichloride complexes (Fe1–Fe3) bearing 2‐(pyridin‐2‐yl)‐4,5‐dihydrooxazole (L1), 4‐isopropyl‐2‐(pyridin‐2‐yl)‐4,5‐dihydrooxazole (L2), and 4‐(t‐butyl)‐2‐(pyridin‐2‐yl)‐4,5‐dihydrooxazole (L3) and iron(II) acetylacetonate complex (Fe4) bearing L1 were synthesized and characterized by elemental and spectroscopic analyses. Determined by single‐crystal X‐ray crystallography, complex Fe3 adopts an unusual unsymmetrical binuclear core. Upon activation with methylaluminoxane (MAO), the pyridine‐oxazoline (Py‐ox) ligated iron complexes (Fe1–Fe4) showed excellent activity towards isoprene polymerization. Complex Fe1 displayed the highest activity of 8160 kg (mol·h)−1 with 54% of 3,4‐polyisoprene. The ligand environment and counter anion on iron center all displayed significant effects on polymerization activity and selectivity, which reflected the special performance compared with pyridine‐imine. And we propose the possible mechanism through cis‐η4 mode following the σ bond rotation because of the steric effect of t‐butyl substituent of Fe4 to give high trans‐1,4‐polymers. Furthermore, the effects of reaction parameters on the catalytic activity and selectivity were investigated in detail.

Re-Evaluation of Product Outcomes in the Rh-Catalyzed Ring Expansion of Aziridines with N-Sulfonyl-1,2,3-Triazoles.

N-heterocycles are prevalent in pharmaceuticals and natural products, but traditional methods often do not introduce significant stereochemical complexity into the ring. We previously reported a Rh-catalyzed ring expansion of aziridines and N-sulfonyl-1,2,3-triazoles to furnish dehydropiperazines with excellent diastereocontrol. However, later studies employing ketone-containing carbene precursors showed that [3,9]-bicyclic aziridine formation competes with production of the desired heterocyclic scaffolds. In light of these surprising results, our initial findings were re-examined both experimentally and computationally to reveal how noncovalent interactions and restricted bond rotation in the aziridinium ylide intermediate promote this unexpected reaction pathway.

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.

An optimization algorithm for conformer generation based on the bond contribution ranking

Many works in computational drug discovery require the conformer generation of small molecules. Most existing tools aim to generate diverse conformers and deal with all of the rotatable bonds without distinction. There are some problems in existing approaches, such as the combinatorial explosion of conformers along with the number of rotatable bonds increasing and the incomplete sampling of the conformational space. Here, we present an optimized conformer generation algorithm based on the bond contribution ranking (ABCR) to find the optimal conformer under any specified scoring function.Compared with existing methods, our method can improve molecular conformational searching and protein-ligand docking performance. Meanwhile, our method has the same or broader coverage of conformational space in the global conformer sampling. Our research shows it can achieve the optima with small numbers of generated conformers and small numbers of iterations.

Exhaustive Mapping of the Conformational Space of Natural Dipeptides by the DFT-D3//COSMO-RS Method.

We extensively mapped energy landscapes and conformations of 22 (including three His protonation states) proteinogenic α-amino acids in trans configuration and the corresponding 484 (222) dipeptides. To mimic the environment in a protein chain, the N- and C-termini of the studied systems were capped with acetyl and N-methylamide groups, respectively. We systematically varied the main chain dihedral angles (ϕ, ψ) by 40° steps and all side chain angles by 90° or 120° steps. We optimized the molecular geometries with the GFN2-xTB semiempirical (SQM) method and performed single point density functional theory calculations at the BP86-D3/DGauss-DZVP//COSMO-RS level in water, 1-octanol, N,N-dimethylformamide, and n-hexane. For each restrained (nonequilibrium) structure, we also calculated energy gradients (in water) and natural atomic charges. The exhaustive and unprecedented QM-based sampling enabled us to construct Ramachandran plots of quantum mechanical (QM(BP86-D3)//COSMO-RS) energies calculated on SQM structures, for all 506 (484 dipeptides and 22 amino acids) studied systems. We showed how the character of an amino acid side chain influences the conformational space of single amino acids and dipeptides. With clustering techniques, we were able to identify unique minima of amino acids and dipeptides (i.e., minima on the GFN2-xTB potential energy surfaces) and analyze the distribution of their BP86-D3//COSMO-RS conformational energies in all four solvents. We also derived an empirical formula for the number of unique minima based on the overall number of rotatable bonds within each peptide. The final peptide conformer data set (PeptideCs) comprises over 400 million structures, all of them annotated with QM(BP86-D3)//COSMO-RS energies. Thanks to its completeness and unbiased nature, the PeptideCs can serve, inter alia, as a data set for the validation of new methods for predicting the energy landscapes of protein structures. This data set may also prove to be useful in the development and reparameterization of biomolecular force fields. The data set is deposited at Figshare (10.25452/figshare.plus.19607172) and can be accessed using a simple web interface at http://peptidecs.uochb.cas.cz.