PyVibMS: a PyMOL plugin for visualizing vibrations in molecules and solids

Theoretical Study of the Isotope Effect in Optical Rotation

In this work, the isotope effect in optical rotation (OR) is examined by exploring structure-property relationships for H → D substitutions in chiral molecules. While electronic effects serve as the dominant source of optical activity, there is a non-negligible contribution from nuclear vibrations, which changes with isotopic substitution. We employ a test set of 50 small organic molecules: three-membered rings with varying heteroatoms (PCl, PH, S, NCl, NH, O, and NBr) and functional groups (Me, F), and simulations were run at the B3LYP/aug-cc-pVDZ level of theory. The objectives of this work are to determine locations of isotopic substitution that result in significant changes in the vibrational correction to the OR and to evaluate which vibrational modes and electronic response are the major contributors to the isotope effect. Molecules with more polarizable heteroatoms in the ring (e.g., S and P) have the largest change in the vibrational correction compared to the unsubstituted parent molecules. In many cases, isotopic substitution made to the hydrogens on the opposite side of the ring from the functional group provides the largest change in the OR. H/D wagging modes and C vibrations (for D-C centers) are the largest contributors to the isotope effect. This is explained with a molecular orbital decomposition analysis of the OR. The relevant vibrational modes affect the orbital transitions that are already significant at the equilibrium geometry. However, this effect is only large when polarizable heteroatoms are involved because the electron density surrounding them is diffuse enough to feel the subtle effect of change in mass due to isotopic substitution on the relevant vibrational modes.

Target analysis and identification of curcumin against vascular calcification

To investigate the mechanism of curcumin (CUR) on vascular calcification (VC), we screen for common targets of CUR and atherosclerosis and verify the targets genes in vivo and in vitro experiments. The common targets of CUR and AS were screened and obtained using different databases. These target genes were analyzed by GO and KEGG pathway enrichment analysis. PPI network analysis was performed and to analyze the key targets. A rat VC model was constructed and CUR was fed for three weeks. The changes of vascular structure and calcium salt deposition were observed in H&E and Von Kossa staining. Further, the expression of these target proteins was detected in the primary VSMCs of VC. The 31 common targets were obtained. GO functional enrichment analysis obtained 1284 terms and KEGG pathway enriched 66 pathways. The key genes were identified in the cytoHubba plugin. The molecular docking analysis showed that CUR bound strongly to EGFR, STAT3 and BCL2. The animal experiments showed the deposition calcium salt reduced by the CUR administration. These proteins BMP2, RUNX2, EGFR, STAT3 and BAX expression were upregulated in VC group and CUR attenuated the upregulated expression. The signal protein Akt and p65 expression increased in VC group and decreased in CUR group. We identified some common target genes of CUR and AS and identified these key genes. The anti-VC effect of CUR was associated with the inhibition of upregulation of EGFR, STAT3 and RUNX2 expression in VSMCs.

Python tools for structural tasks in chemistry

In recent decades, the use of computational approaches and artificial intelligence in the scientific environment has become more widespread. In this regard, the popular and versatile programming language Python has attracted considerable attention from scientists in the field of chemistry. It is used to solve a variety of chemical and structural problems, including calculating descriptors, molecular fingerprints, graph construction, and computing chemical reaction networks. Python offers high-quality visualization tools for analyzing chemical spaces and compound libraries. This review is a list of tools for the above tasks, including scripts, libraries, ready-made programs, and web interfaces. Inevitably this manuscript does not claim to be an all-encompassing handbook including all the existing Python-based structural chemistry codes. The review serves as a starting point for scientists wishing to apply automatization or optimization to routine chemistry problems.

A-Band Absorption Spectrum of the ClSO Radical: Electronic Structure of the Sulfinyl Group

Sulfur oxide species (RSOx) play a critical role in many fields, ranging from biology to atmospheric chemistry. Chlorine-containing sulfur oxides may play a key role in sulfate aerosol formation in Venus' cloud layer by catalyzing the oxidation of SO to SO2 via sulfinyl radicals (RSO). We present results from the gas-phase UV-vis transient absorption spectroscopy study of the simplest sulfinyl radical, ClSO, generated from the pulsed-laser photolysis of thionyl chloride at 248 nm (at 40 Torr of N2 and 292 K). A weak absorption spectrum from 350 to 480 nm with a peak at 385 nm was observed, with partially resolved vibronic bands (spacing = 226 cm-1), and a peak cross section σ(385 nm) = (7.6 ± 1.9) × 10-20 cm2. From ab initio calculations at the EOMEE-CCSD/ano-pVQZ level, we assigned this band to 12A' ← X2A″ and 22A' ← X2A″ transitions. The spectrum was modeled as a sum of a bound-to-free transition to the 12A' state and a bound-to-bound transition to the 22A' state with similar oscillator strengths; the prediction agreed well with the observed spectrum. We attributed the vibronic structure to a progression in the bending vibration of the 22A' state. Further calculations at the XDW-CASPT2 level predicted a conical intersection between the excited 12A' and 22A' potential energy surfaces near the Franck-Condon region. The geometry of the minimum-energy conical intersection was similar to that of the ground-state geometry. The lack of structure at shorter wavelengths could be evidence of a short excited-state lifetime arising from strong vibronic coupling. From simplified molecular orbital analysis, we attributed the ClSO spectrum to transitions involving the out-of-plane π/π* orbitals along the S-O bond and the in-plane orbital possessing a σ/σ* character along the S-Cl bond. We hypothesize that these orbitals are common to other sulfinyl radicals, RSO, which would share a combination of a strong and a weak transition in the UV (near 300 nm) and visible (400-600 nm) regions.

Identification of novel inhibitors from Urtica spp against TNBC targeting JAK2 receptor for breast cancer therapy

Breast cancer is the most prevalent form of cancer in women globally, and TNBC (triple-negative breast cancer) is its aggressive type since it lacks the usual targets. JAK2/STAT3 pathway can be an important lead in anticancer drug discovery, as restraining the downstream signalling of this pathway results in the induction of cell apoptosis. Moreover, various limitations associated with chemotherapy are the reason to find an alternative herbal-based therapy. For this study, we collected Urtica dioica and U. parviflora from different regions of Uttarakhand, followed by preparation of their leaf and stem extracts in different solvents. The GC-MS analysis of these extracts revealed a total of 175 compounds to be present in them. Further, by molecular docking approach, we studied the interaction between these compounds and JAK2, and 12 major compounds with better binding energy than the control Paclitaxel were identified. In addition, the selected hits were also reported to display better pharmacokinetic properties. Moreover, extracts from both the Urtica spp. displayed significant anticancer activity against MDA-MB-231(TNBC cell line) and exhibited lower cytotoxicity in healthy cell lines, i.e. HEK293T, indicating that these extracts were safer to use. Hence, the findings in our study can be crucial in the area of herbal-based target-specific drug development against breast cancer.

Structure-based virtual screening for identification of potential non-steroidal LXR modulators against neurodegenerative conditions

Liver X Receptors (LXRs) are members of the nuclear receptor superfamily that regulate cholesterol metabolism. LXRs have been suggested as promising targets against many neurodegenerative diseases (NDDs). The present study was aimed to identify novel non-steroidal molecules that may potentially modulate LXR activity. The structure-based virtual screening (SBVS) was used to search for suitable compounds from the Asinex library. The top hits were selected and filtered based on their binding affinity for LXR α and β isoforms. Based on molecular docking and scoring results, 24 compounds were selected that had binding energy in the range of - 13.9 to - 12 for LXRα and - 12.5 to - 11 for LXRβ, which were higher than the reference ligands (GW3965 and TO901317). Further, the five hits referred to as model 29, 64, 202, 250, 313 were selected by virtue of their binding interactions with amino acid residues at the active site of LXRs. The selected hits were then subjected to absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis and blood-brain permeability prediction. It was observed that the selected hits had better pharmacokinetic properties with no toxicity and could cross blood-brain barrier. Further, the selected hits were analysed for dynamic evolution of the system with LXRs by molecular dynamics (MD) simulation at 100 ns using GROMACS. The MD simulation results validated that selected hits possess a remarkable amount of flexibility, stability, compactness, binding energy and exhibited limited conformational modification. The root mean square deviation (RMSD) values of the top-scoring hits complexed with LXRα and LXRβ were 0.05-0.6 nm and 0.05-0.45 nm respectively, which is greater than the protein itself. Altogether the study identified potential non-steroidal LXR modulators that appear to be effective against various neurodegenerative conditions involving perturbed cholesterol and lipid homeostasis.

Antagonistic Effect and In Vitro Activity of Dauricine on Glucagon Receptor

Abnormal increases in glucagon (GCG) are the primary cause of type II diabetes mellitus. When GCG interacts with a glucagon receptor (GCGR), GCG can increase the blood glucose level. In this paper, a compound that could interfere with the binding of GCG and GCGR to inhibit the increase of blood glucose was investigated. First, molecular docking was used to conduct preliminary screening of compounds whose active components could combine with GCGR by AutoDock Vina. The binding of the receptor-ligand complex was analyzed by PyMOL. Results showed that dauricine could tightly bind to the receptor pocket. Second, the plasmid pcDNA3.1(+)-GCGR containing the target gene was transfected into HEK293 cells for expression, which was the cell model established to screen GCGR antagonist. Dauricine, the lead compound of glucagon receptor antagonist (GRA), was screened using the GRA screening model in vitro. Finally, using [Des-His1, Glu9]-Glucagon amide as the positive control, flow cytometry was used to express the antagonistic effect of the compound. Consequently, dauricine can antagonize the GCGR.

Mechanistic Details of the Sharpless Epoxidation of Allylic Alcohols—A Combined URVA and Local Mode Study

In this work, we investigated the catalytic effects of a Sharpless dimeric titanium (IV)–tartrate–diester catalyst on the epoxidation of allylalcohol with methyl–hydroperoxide considering four different orientations of the reacting species coordinated at the titanium atom (reactions R1–R4) as well as a model for the non-catalyzed reaction (reaction R0). As major analysis tools, we applied the URVA (Unified Reaction Valley Approach) and LMA (Local Mode Analysis), both being based on vibrational spectroscopy and complemented by a QTAIM analysis of the electron density calculated at the DFT level of theory. The energetics of each reaction were recalculated at the DLPNO-CCSD(T) level of theory. The URVA curvature profiles identified the important chemical events of all five reactions as peroxide OO bond cleavage taking place before the TS (i.e., accounting for the energy barrier) and epoxide CO bond formation together with rehybridization of the carbon atoms of the targeted CC double bond after the TS. The energy decomposition into reaction phase contribution phases showed that the major effect of the catalyst is the weakening of the OO bond to be broken and replacement of OH bond breakage in the non-catalyzed reaction by an energetically more favorable TiO bond breakage. LMA performed at all stationary points rounded up the investigation (i) quantifying OO bond weakening of the oxidizing peroxide upon coordination at the metal atom, (ii) showing that a more synchronous formation of the new CO epoxide bonds correlates with smaller bond strength differences between these bonds, and (iii) elucidating the different roles of the three TiO bonds formed between catalyst and reactants and their interplay as orchestrated by the Sharpless catalyst. We hope that this article will inspire the computational community to use URVA complemented with LMA in the future as an efficient mechanistic tool for the optimization and fine-tuning of current Sharpless catalysts and for the design new of catalysts for epoxidation reactions.

Oligomeric interactions maintain active-site structure in a noncooperative enzyme family

The evolutionary benefit accounting for widespread conservation of oligomeric structures in proteins lacking evidence of intersubunit cooperativity remains unclear. Here, crystal and cryo-EM structures, and enzymological data, demonstrate that a conserved tetramer interface maintains the active-site structure in one such class of proteins, the short-chain dehydrogenase/reductase (SDR) superfamily. Phylogenetic comparisons support a significantly longer polypeptide being required to maintain an equivalent active-site structure in the context of a single subunit. Oligomerization therefore enhances evolutionary fitness by reducing the metabolic cost of enzyme biosynthesis. The large surface area of the structure-stabilizing oligomeric interface yields a synergistic gain in fitness by increasing tolerance to activity-enhancing yet destabilizing mutations. We demonstrate that two paralogous SDR superfamily enzymes with different specificities can form mixed heterotetramers that combine their individual enzymological properties. This suggests that oligomerization can also diversify the functions generated by a given metabolic investment, enhancing the fitness advantage provided by this architectural strategy.

On the use of a volume constraint to account for thermal expansion effects on the low-frequency vibrations of molecular crystals

A volume-constraint method is presented as a means to capture the influence of thermal expansion on the low-frequency vibrations in molecular crystals. In particular, the room-temperature terahertz absorption spectra of L-tartaric acid, α-lactose monohydrate, and α-para-aminobenzoic acid (PABA) have been simulated using dispersion-corrected, solid-state density functional theory (DFT-D). By comparing the normal modes obtained with a unit cell optimised without constraints to those obtained with a unit cell optimised while constrained to keep its experimental volume, wholesale improvements to the resultant spectrum is achieved when using the constrained geometry by inhibiting cell contraction. These improvements are demonstrated over a range of popular density functionals and basis sets up to triple-zeta complexity. A correlation method is then presented as a means to quantitatively compare the vibrational pattern of normal modes obtained from both unit cells. This analysis reveals that thermal expansion can effect the character and relative frequency of normal modes, with the choice of geometry ultimately affecting the assignment of the experimental absorptions. The sensibility of using the experimental volume as an approximation is then discussed, where it is speculated that large basis sets or hybrid functionals are necessary to ensure that the thermal expansion effect is not overestimated. The low-frequency absorption spectrum of PABA is then fully characterised using the PBE-D3BJ/6-311G(2d,2p) method.

BF3–Catalyzed Diels–Alder Reaction between Butadiene and Methyl Acrylate in Aqueous Solution—An URVA and Local Vibrational Mode Study

In this study we investigate the Diels–Alder reaction between methyl acrylate and butadiene, which is catalyzed by BF3 Lewis acid in explicit water solution, using URVA and Local Mode Analysis as major tools complemented with NBO, electron density and ring puckering analyses. We considered four different starting orientations of methyl acrylate and butadiene, which led to 16 DA reactions in total. In order to isolate the catalytic effects of the BF3 catalyst and those of the water environment and exploring how these effects are synchronized, we systematically compared the non-catalyzed reaction in gas phase and aqueous solution with the catalyzed reaction in gas phase and aqueous solution. Gas phase studies were performed at the B3LYP/6-311+G(2d,p) level of theory and studies in aqueous solution were performed utilizing a QM/MM approach at the B3LYP/6-311+G(2d,p)/AMBER level of theory. The URVA results revealed reaction path curvature profiles with an overall similar pattern for all 16 reactions showing the same sequence of CC single bond formation for all of them. In contrast to the parent DA reaction with symmetric substrates causing a synchronous bond formation process, here, first the new CC single bond on the CH2 side of methyl acrylate is formed followed by the CC bond at the ester side. As for the parent DA reaction, both bond formation events occur after the TS, i.e., they do not contribute to the energy barrier. What determines the barrier is the preparation process for CC bond formation, including the approach diene and dienophile, CC bond length changes and, in particular, rehybridization of the carbon atoms involved in the formation of the cyclohexene ring. This process is modified by both the BF3 catalyst and the water environment, where both work in a hand-in-hand fashion leading to the lowest energy barrier of 9.06 kcal/mol found for the catalyzed reaction R1 in aqueous solution compared to the highest energy barrier of 20.68 kcal/mol found for the non-catalyzed reaction R1 in the gas phase. The major effect of the BF3 catalyst is the increased mutual polarization and the increased charge transfer between methyl acrylate and butadiene, facilitating the approach of diene and dienophile and the pyramidalization of the CC atoms involved in the ring formation, which leads to a lowering of the activation energy. The catalytic effect of water solution is threefold. The polar environment leads also to increased polarization and charge transfer between the reacting species, similar as in the case of the BF3 catalyst, although to a smaller extend. More important is the formation of hydrogen bonds with the reaction complex, which are stronger for the TS than for the reactant, thus stabilizing the TS which leads to a further reduction of the activation energy. As shown by the ring puckering analysis, the third effect of water is space confinement of the reacting partners, conserving the boat form of the six-member ring from the entrance to the exit reaction channel. In summary, URVA combined with LMA has led to a clearer picture on how both BF3 catalyst and aqueous environment in a synchronized effort lower the reaction barrier. These new insights will serve to further fine-tune the DA reaction of methyl acrylate and butadiene and DA reactions in general.

LModeA-nano: A PyMOL Plugin for Calculating Bond Strength in Solids, Surfaces, and Molecules via Local Vibrational Mode Analysis

The analysis of chemical bonding in crystal structures and surfaces is an important research topic in theoretical chemistry. In this work, we present a PyMOL plugin, named LModeA-nano, as implementation of the local vibrational mode theory for periodic systems (Tao et al. J. Chem. Theory Comput. 2019, 15, 1761) assessing bond strength in terms of local stretching force constants in extended systems of one, two, and three dimensions. LModeA-nano can also analyze chemical bonds in isolated molecular systems thus enabling a head-to-head comparison of bond strength across systems with different dimensions in periodicity (0-3D). The new code is interfaced to the output generated by various solid-state modeling packages including VASP, CP2K, Quantum ESPRESSO, CASTEP, and CRYSTAL. LModeA-nano is cross-platform, open-source and freely available on GitHub: https://github.com/smutao/LModeA-nano.