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We introduce in this work a unique parameter for the quantitative assessment of the intrinsic strength of the [pi] interaction between two monomers forming a complex. The new parameter is a local intermonomer stretching force constant, based on the local mode theory, originally developed by Konkoli and Cremer, and derived from the set of nine possible intermonomer normal vibrational modes. The new local force constant was applied to a diverse set of more than 70 molecular complexes, which was divided into four groups. Group 1 includes atoms, ions, and small molecules interacting with benzene and substituted benzenes. Group 2 includes transition metal hydrides and oxides interacting with benzene while Group 3 involves ferrocenes, chromocenes, and titanium sandwich compounds. Group 4 presents an extension to oxygen [pi]-hole interactions in comparison with in-plane hydrogen bonding. We found that the strength of the [pi] interactions in these diverse molecular complexes can vary from weak interactions with predominantly electrostatic character, found, e.g., for argon-benzene complexes, to strong interactions with a substantial covalent nature, found, e.g., for ferrocenes; all being seamlessly described and compared with the new intermonomer local mode force constant, which also outperforms other descriptors such as an averaged force constant or a force constant guided by the electron density bond paths. We hope that our findings will inspire the community to apply the new parameter also to other intermonomer [pi] interactions, enriching in this way the broad field of organometallic chemistry with a new efficient assessment tool. Key words: local mode analysis, intermonomer force constant, sandwich complexes, vibrational spectroscopy, Introduction Noncovalent interactions between monomers leading to complex formation is the topic of many experimental and computational investigations, because of the vital role they play in the structure and properties [...]

Cobalt-free manganese-based lithium-rich layered oxides (LLOs) have garnered research attention as prospective lithium-ion cathode materials owing to their large specific capacity and low price. However, their large-scale application is hindered by their low Coulombic efficiency, poor cycling performance, voltage attenuation, and structural phase transition. To address these issues, the LLO structure is modified via Ti doping at the manganese site herein. Ti-doped Li1.2Mn0.6−xTixNi0.2O2 (x = 0, 0.03, 0.05, 0.10, and 0.15) is prepared using the high-temperature solid-state method. The Ti-doped Li1.2Mn0.6Ni0.2O2 is calculated via first principles. The results show that Ti4+ doping improves the cycle stability and rate performance of Li1.2Mn0.6Ni0.2O2. Electrochemical test results show that the sample exhibits enhanced electrochemical performance when the Ti doping amount is 0.05. The discharge specific capacity at 0.1C is 210.4 mAh·g−1, which reaches 191.1 mAh·g−1 after 100 cycles, with a capacity retention rate of 90.7%. This study proves the feasibility of using cheap cobalt-free LLOs as cathode materials for LIBs and provides a novel system for exploiting low-cost and high-performance cathode materials. [ABSTRACT FROM AUTHOR]

We introduce in this work a unique parameter for the quantitative assessment of the intrinsic strength of the π interaction between two monomers forming a complex. The new parameter is a local intermonomer stretching force constant, based on the local mode theory, originally developed by Konkoli and Cremer, and derived from the set of nine possible intermonomer normal vibrational modes. The new local force constant was applied to a diverse set of more than 70 molecular complexes, which was divided into four groups. Group 1 includes atoms, ions, and small molecules interacting with benzene and substituted benzenes. Group 2 includes transition metal hydrides and oxides interacting with benzene while Group 3 involves ferrocenes, chromocenes, and titanium sandwich compounds. Group 4 presents an extension to oxygen π–hole interactions in comparison with in-plane hydrogen bonding. We found that the strength of the π interactions in these diverse molecular complexes can vary from weak interactions with predominantly electrostatic character, found, e.g., for argon–benzene complexes, to strong interactions with a substantial covalent nature, found, e.g., for ferrocenes; all being seamlessly described and compared with the new intermonomer local mode force constant, which also outperforms other descriptors such as an averaged force constant or a force constant guided by the electron density bond paths. We hope that our findings will inspire the community to apply the new parameter also to other intermonomer π interactions, enriching in this way the broad field of organometallic chemistry with a new efficient assessment tool. [ABSTRACT FROM AUTHOR]

The conformational properties of ring compounds such as cycloalkanes determine to a large extent their stability and reactivity. Therefore, the investigation of conformational processes such as ring inversion and/or ring pseudorotation has attracted a lot of attention over the past decades. An in-depth conformational analysis of ring compounds requires mapping the relevant parts of the conformational energy surface at stationary and also at non-stationary points. However, the latter is not feasible by a description of the ring with Cartesian or internal coordinates. We provide in this work, a solution to this problem by introducing a new coordinate system based on the Cremer–Pople puckering and deformation coordinates. Furthermore, analytic first- and second-order derivatives of puckering and deformation coordinates, i.e., B-matrices and D-tensors, were developed simplifying geometry optimization and frequency calculations. The new coordinate system is applied to map the potential energy surfaces and reaction paths of cycloheptane (C7H14), cyclooctane (C8H16), and cyclo[18]carbon (C18) at the quantum chemical level and to determine for the first time all stationary points of these ring compounds in a systematic way. [ABSTRACT FROM AUTHOR]

Conceptually mimicking biomolecules' ability to construct multiple‐helical aggregates with emergent properties and functions remains a long‐standing challenge. Here we report an atom‐precise 18‐copper nanocluster (NC), Cu18H(PET)14(TPP)6(NCS)3 (Cu18H) which contains a pseudo D3‐symmetrical triple‐helical Cu15 core. Structurally, Cu18H may be also viewed as sandwich type of sulfur‐bridged chiral copper cluster units [Cu6−Cu6−Cu6], endowing three‐layered 3D chirality. More importantly, the chiral NCs are aggregated into an infinite double‐stranded helix supported by intra‐strand homonuclear C−H⋅⋅⋅H−C dihydrogen contacts and inter‐strand C−H/π and C−H/S interactions. The unique multi‐layered 3D chirality and the double‐helical assembly of Cu18H are evocative of DNA. Moreover, the collective behaviours of the aggregated NCs not only exhibit crystallization‐induced emission enhancement (CIEE) and aggregation‐induced emission enhancement (AIEE) effects in the deep‐red region, but also efficiently catalyze electron transfer (ET) reaction. This study thus presents that hierarchical assemblies of atomically defined copper NCs could be intricate as observed for important biomolecules like DNA with emergent properties arising from aggregated behaviours. [ABSTRACT FROM AUTHOR]

We report a comprehensive investigation of the 5-androstene-3,17-dione to 4-androstene-3,17-dione isomerization in Ketosteroid Isomerase, gas phase and aqueous solution, applying as tools the Unified Reaction Valley Approach (URVA) and the Local Vibrational Mode Analysis. Conformational changes of the steroid rings are monitored via Cremer-Pople puckering coordinates. URVA identifies simultaneous breakage of the C α –H bond and O–H bond formation with the catalytic acid, leading to an intermediate with the acid positioned over ring A as the major chemical events of the first reaction step. Via a barrier-less shift, a second intermediate is formed with the acid being positioned over ring B. Then, according to URVA, breakage of the intermediate O–H bond, the formation of the new C γ –H bond accompanied by a double bond shift in rings A and B forms the major chemical events of the second reaction step, which is facilitated by favorable ring puckering. Reactions in protein and gas phase have comparable activation enthalpies, whereas the barrier in aqueous solution is higher, confirming that the major task of the enzyme pocket is to shield the migrating hydrogen atom and the catalyzing acid from interactions with solvent molecules diluting the catalytic power. We do not find exceptional H-bonding with Asp99 and Tyr14, excluding their catalytic activity. There is no strong hydrogen bonding in the TS, which could account for lowering the activation barrier. Our study provides a clear picture of the isomerization process, which will also inspire similar investigations of other important enzymatic reactions. We present a computational study of a substrate isomerization catalyzed by Ketosteroid Isomerase based on QM/MM calculations, our Unified Reaction Valley Approach and Local Vibrational Mode Analysis. In summary, our study quantifies Talaly's postulate that the major role of the enzyme pocket is to shield the migrating hydrogen atom from interactions with solvent molecules. Our analysis further confirms that there is no exceptional hydrogen bonding between the substrate and surrounding enzyme amino acids, which could account for lowering the activation barrier. [ABSTRACT FROM AUTHOR]

We evaluate the correlation between binding energy (BE) and electron density ρ(r) at the bond critical point for 28 neutral hydrogen bonds, recently reported by Emamian and co‐workers (J. Comput. Chem., 2019, 40, 2868). As an efficient tool, we use local stretching force constant kHBa derived from the local vibrational mode theory of Konkoli and Cremer. We compare the physical nature of BE versus kHBa, and provide an important explanation for cases with significant deviation in the BE– kHBa relation as well as in the BE–ρ(r) correlation. We also show that care has to be taken when different hydrogen bond strength measures are compared. The BE is a cumulative hydrogen bond strength measure while kHBa is a local measure of hydrogen bond strength covering different aspects of bonding. A simplified and unified description of hydrogen bonding is not always possible and needs an in‐depth understanding of the systems involved. [ABSTRACT FROM AUTHOR]

Under the assistance of the state‐of‐the‐art meta‐dynamics simulations, in this contribution, we report a push‐pull‐type acylhydrazone 4(Z) ([Z)‐2‐(naphthalen‐2‐yloxy)‐N'‐(pyridine‐2‐ylmethylene)acetohydrazide] connecting an electron‐donating naphthalene ether group with an accepting pyridyl unit, which could be thermally converted to its configurational isomer 4(E) ([E)‐2‐(naphthalen‐2‐yloxy)‐N'‐(pyridine‐2‐ylmethylene)acetohydrazide]. The thermally triggered Z‐to‐E configurational isomerization not only involves up to five chemical bonds undergoing 180° rotation in the backbone of acylhydrazone, but changes the crystal packing symmetry from a centrosymmetric space group to a non‐centrosymmetric one. Most impressively, the acentric crystal arrangement of 4(E) exhibits a second‐harmonic generation (SHG) active response, about 2.5 times than that of KH2PO4 (KDP) standard. [ABSTRACT FROM AUTHOR]

Benzene and acetonitrile are two of the most commonly used solvents found in almost every chemical laboratory. Titan is one other place in the solar system that has large amounts of these compounds. On Titan, organic molecules are produced in the atmosphere and carried to the surface where they can mineralize. Here, we report the phase diagram of mixtures of acetonitrile and benzene, and provide an account of the structure and composition of the phases. To mimic the environment on Titan more accurately, we tested the stability of the structure under liquid ethane. The results provide new insights into the structure and stability of potential extraterrestrial minerals. In light of Dragonfly, NASA's upcoming mission to Titan, revisiting the fundamental chemistry of the smallest molecules with modern methods and techniques can have significant contributions to this epochal mission and can open new research directions in chemistry. [ABSTRACT FROM AUTHOR]

Visualizing vibrational motions calculated with different ab initio packages requires dedicated post-processing tools. Here, we present a PyMOL plugin called PyVibMS for visualizing the vibrational motions for both molecular and solid systems calculated by mainstream quantum chemical computer programs including Gaussian, Q–Chem, VASP, and CRYSTAL. Benefiting from the continuing development of the PyMOL platform, PyVibMS provides powerful functionalities and user-friendly interface. PyVibMS was written in Python and its open-source nature makes it flexible and sustainable. As an example, the motions of the Konkoli-Cremer local vibrational modes are shown in this work for the first time. PyVibMS is freely available at https://github.com/smutao/PyVibMS. [ABSTRACT FROM AUTHOR]

Modern vibrational spectroscopy is more than just an analytical tool. Information about the electronic structure of a molecule, the strength of its bonds, and its conformational flexibility is encoded in the normal vibrational modes. On the other hand, normal vibrational modes are generally delocalized, which hinders the direct access to this information, attainable only via local vibration modes and associated local properties. Konkoli and Cremer provided an ingenious solution to this problem by deriving local vibrational modes from the fundamental normal modes, obtained in the harmonic approximation of the potential, via mass‐decoupled Euler–Lagrange equations. This review gives a general introduction into the local vibrational mode theory of Konkoli and Cremer, elucidating how this theory unifies earlier attempts to obtain easy to interpret chemical information from vibrational spectroscopy: (a) the local mode theory furnishes bond strength descriptors derived from force constant matrices with a physical basis, (b) provides the highly sought after extension of the Badger rule to polyatomic molecules, (c) and offers a simpler way to derive localized vibrations compared to the complex route via overtone spectroscopy. Successful applications are presented, including a new measure of bond strength, a new detailed analysis of infrared/Raman spectra, and the recent extension to periodic systems, opening a new avenue for the characterization of bonding in crystals. At the end of this review the LMODEA software is introduced, which performs the local mode analysis (with minimal computational costs) after a harmonic vibrational frequency calculation optionally using measured frequencies as additional input. This article is categorized under:Structure and Mechanism > Molecular StructuresTheoretical and Physical Chemistry > SpectroscopySoftware > Quantum ChemistryElectronic Structure Theory > Ab Initio Electronic Structure Methods [ABSTRACT FROM AUTHOR]

The synthesis and structure of a giant 102‐silver‐atom nanocluster (NC) 1 is presented. X‐ray structural analysis reveals that 1 features a multi‐shelled metallic core of Ag6@Ag24@Ag60@Ag12. An octahedral Ag6 core is encaged by a truncated octahedral Ag24 shell. The Ag24 shell is composed of a hitherto unknown sodalite‐type silver orthophosphate cluster (SOC) {(Ag3PO4)8}, reminiscent of the Ag3PO4 photocatalyst. The SOC is capped by six interstitial sulfur atoms, giving a unique anionic cluster [Ag6@{(Ag3PO4)8}S6]6−, which functions as an intricate polyhedral template with abundant surface O and S atoms guiding the formation of a rare rhombicosidodecahedral Ag60 shell. An array of 6 linear Ag2 staples further surround this Ag60 shell. [Ag6@{(Ag3PO4)8}S6]6− is an unusual Ag‐based templating anion to induce the assembly of a SOC within silver NC. This finding provides molecular models for bulk Ag3PO4, and offers a fresh template strategy for the synthesis of silver NCs with high symmetry. [ABSTRACT FROM AUTHOR]

The Bacillus subtilis chorismate mutase catalysed Claisen rearrangement of chorismate to prephenate is one of the few pericyclic processes in biology, and as such provides a rare opportunity for understanding how Nature promotes such rearrangements so successfully. The major focus of this work is on (i) Exploring the hypothesis that the mechanism of the chorismate rearrangement is the same in the gas phase, in the aqueous solution and in the enzyme; (ii) Investigating current suggestions that the enzyme lowers the barrier via transition state stabilisation rather than via space confinement; and (iii) A comparison of Nature's way of catalysing the reaction with a gold(I) catalysed chorismate rearrangement. Based the Unified Reaction Valley Approach (URVA), for the first time, a detailed one-to-one comparison of the rearrangement in the gas phase, in the aqueous solution and in the enzyme is presented. URVA confirms that the actual chemical process of CO bond breaking and CC bond forming is the same for all media and unravels the unique catalytic function of the enzyme as a combination of shortening the process of positioning the enolpyruvyl side chain over the cyclohexadienyl ring by space confinement in concert with facilitating CO cleavage by enhanced charge polarisation. The transition state does not play a signifiant role for the rearrangement. In contrast, the gold catalyst changes the chemical process. The rearrangement is split into two steps by switching between Au[I]-π and Au[I]-σ complexation, thus avoiding the energy consuming CO breakage in the first step. Suggestions are made for metalloenzyme analogues combining both strategies. [ABSTRACT FROM AUTHOR]

Using catastrophe theory and the concept of a mutation path, an algorithm is developed that leads to the direct correlation of the normal vibrational modes of two structurally related molecules. The mutation path is defined by weighted incremental changes in mass and geometry of the molecules in question, which are successively applied to mutate a molecule into a structurally related molecule and thus continuously converting their normal vibrational spectra from one into the other. Correlation diagrams are generated that accurately relate the normal vibrational modes to each other by utilizing mode-mode overlap criteria and resolving allowed and avoided crossings of vibrational eigenstates. The limitations of normal mode correlation, however, foster the correlation of local vibrational modes, which offer a novel vibrational measure of similarity. It will be shown how this will open new avenues for chemical studies. © 2017 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

A hexapeptide derived from an enzyme inhibitor was used as an affinity ligand for the conjugation of a hydrophilic polymer to the enzyme. The peptide targeted the polymer to the “berth” of the inhibitor in the enzyme, affording the enzyme resistance to the inhibitor without affecting the enzymatic activity. [ABSTRACT FROM AUTHOR]

Palbociclib (PAL) is an effective anti-breast cancer drug, but its use has been partly restricted due to poor bioavailability (resulting from extremely low water solubility) and serious adverse reactions. In this study, two cocrystals of PAL with resorcinol (RES) or orcinol (ORC) were prepared by evaporation crystallization to enhance their solubility. The cocrystals were characterized by single crystal X-ray diffraction, Hirshfeld surface analysis, powder X-ray diffraction, differential scanning calorimetry, thermogravimetric analysis, Fourier transform infrared and scanning electron microscopy. The intrinsic dissolution rates of the PAL cocrystals were determined in three different dissolution media (pH 1.0, pH 4.5 and pH 6.8), and both cocrystals showed improved dissolution rates at pH 1.0 and pH 6.8 in comparison to the parent drug. In addition, the cocrystals increased the solubility of PAL at pH 6.8 by 2–3 times and showed good stabilities in both the accelerated stability testing and stress testing. The PAL-RES cocrystal also exhibited an improved relative bioavailability (1.24 times) than PAL in vivo pharmacokinetics in rats. Moreover, the in vitro cytotoxicity assay of PAL-RES showed an increased IC50 value for normal cells, suggesting a better biosafety profile than PAL. Co-crystallization may represent a promising strategy for improving the physicochemical properties of PAL with better pharmacokinetics. [ABSTRACT FROM AUTHOR]

Computational prediction of Protein-Ligand Interaction (PLI) is an important step in the modern drug discovery pipeline as it mitigates the cost, time, and resources required to screen novel therapeutics. Deep Neural Networks (DNN) have recently shown excellent performance in PLI prediction. However, the performance is highly dependent on protein and ligand features utilized for the DNN model. Moreover, in current models, the deciphering of how protein features determine the underlying principles that govern PLI is not trivial. In this work, we developed a DNN framework named SSnet that utilizes secondary structure information of proteins extracted as the curvature and torsion of the protein backbone to predict PLI. We demonstrate the performance of SSnet by comparing against a variety of currently popular machine and non-Machine Learning (ML) models using various metrics. We visualize the intermediate layers of SSnet to show a potential latent space for proteins, in particular to extract structural elements in a protein that the model finds influential for ligand binding, which is one of the key features of SSnet. We observed in our study that SSnet learns information about locations in a protein where a ligand can bind, including binding sites, allosteric sites and cryptic sites, regardless of the conformation used. We further observed that SSnet is not biased to any specific molecular interaction and extracts the protein fold information critical for PLI prediction. Our work forms an important gateway to the general exploration of secondary structure-based Deep Learning (DL), which is not just confined to protein-ligand interactions, and as such will have a large impact on protein research, while being readily accessible for de novo drug designers as a standalone package. [ABSTRACT FROM AUTHOR]

Seventeen singlet excited states of ethylene have been calculated via time-dependent density functional theory (TDDFT) with the CAM-B3LYP functional and the geometries of 11 excited states were optimized successfully. The local vibrational mode theory was employed to examine the intrinsic C=C/C–H bond strengths and their change upon excitation. The natural transition orbital (NTO) analysis was used to further analyze the C=C/C–H bond strength change in excited states versus the ground state. For the first time, three excited states including π y ′ → 3s, π y ′ → 3p y and π y ′ → 3p z were identified with stronger C=C ethylene double bonds than in the ground state. [ABSTRACT FROM AUTHOR]

11 aryl–lone pair and three aryl–anion π –hole interactions are investigated, along with the argon–benzene dimer and water dimer as reference compounds, utilizing the local vibrational mode theory, originally introduced by Konkoli and Cremer, to quantify the strength of the π –hole interaction in terms of a new local vibrational mode stretching force constant between the two engaged monomers, which can be conveniently used to compare different π –hole systems. Several factors have emerged which influence strength of the π –hole interactions, including aryl substituent effects, the chemical nature of atoms composing the aryl rings/ π –hole acceptors, and secondary bonding interactions between donors/acceptors. Substituent effects indirectly affect the π –hole interaction strength, where electronegative aryl-substituents moderately increase π –hole interaction strength. N-aryl members significantly increase π –hole interaction strength, and anion acceptors bind more strongly with the π –hole compared to charge neutral acceptors (lone–pair donors). Secondary bonding interactions between the acceptor and the atoms in the aryl ring can increase π –hole interaction strength, while hydrogen bonding between the π –hole acceptor/donor can significantly increase or decrease strength of the π –hole interaction depending on the directionality of hydrogen bond donation. Work is in progress expanding this research on aryl π –hole interactions to a large number of systems, including halides, CO, and OCH3− as acceptors, in order to derive a general design protocol for new members of this interesting class of compounds. [ABSTRACT FROM AUTHOR]

The unified reaction valley approach (URVA) differs from mainstream mechanistic studies, as it describes a chemical reaction via the reaction path and the surrounding reaction valley on the potential energy surface from the van der Waals region to the transition state and far out into the exit channel, where the products are located. The key feature of URVA is the focus on the curving of the reaction path. Moving along the reaction path, any electronic structure change of the reacting molecules is registered by a change in their normal vibrational modes and their coupling with the path, which recovers the curvature of the reaction path. This leads to a unique curvature profile for each chemical reaction with curvature minima reflecting minimal change and curvature maxima, the location of important chemical events such as bond breaking/forming, charge polarization and transfer, rehybridization, etc. A unique decomposition of the path curvature into internal coordinate components provides comprehensive insights into the origins of the chemical changes taking place. After presenting the theoretical background of URVA, we discuss its application to four diverse catalytic processes: (i) the Rh catalyzed methanol carbonylation—the Monsanto process; (ii) the Sharpless epoxidation of allylic alcohols—transition to heterogenous catalysis; (iii) Au(I) assisted [3,3]-sigmatropic rearrangement of allyl acetate; and (iv) the Bacillus subtilis chorismate mutase catalyzed Claisen rearrangement—and show how URVA leads to a new protocol for fine-tuning of existing catalysts and the design of new efficient and eco-friendly catalysts. At the end of this article the pURVA software is introduced. The overall goal of this article is to introduce to the chemical community a new protocol for fine-tuning existing catalytic reactions while aiding in the design of modern and environmentally friendly catalysts. [ABSTRACT FROM AUTHOR]

Over the past two decades, the vibrational Stark effect has become an important tool to measure and analyze the in situ electric field strength in various chemical environments with infrared spectroscopy. The underlying assumption of this effect is that the normal stretching mode of a target bond such as CO or CN of a reporter molecule (termed vibrational Stark effect probe) is localized and free from mass-coupling from other internal coordinates, so that its frequency shift directly reflects the influence of the vicinal electric field. However, the validity of this essential assumption has never been assessed. Given the fact that normal modes are generally delocalized because of mass-coupling, this analysis was overdue. Therefore, we carried out a comprehensive evaluation of 68 vibrational Stark effect probes and candidates to quantify the degree to which their target normal vibration of probe bond stretching is decoupled from local vibrations driven by other internal coordinates. The unique tool we used is the local mode analysis originally introduced by Konkoli and Cremer, in particular the decomposition of normal modes into local mode contributions. Based on our results, we recommend 31 polyatomic molecules with localized target bonds as ideal vibrational Stark effect probe candidates. [ABSTRACT FROM AUTHOR]

Periodic local vibrational modes were calculated with the rev-vdW-DF2 density functional to quantify the intrinsic strength of the X-I⋯OA-type halogen bonding (X = I or Cl; OA: carbonyl, ether and N-oxide groups) in 32 model systems originating from 20 molecular crystals. We found that the halogen bonding between the donor dihalogen X-I and the wide collection of acceptor molecules OA features considerable variations of the local stretching force constants (0.1–0.8 mdyn/Å) for I⋯O halogen bonds, demonstrating its powerful tunability in bond strength. Strong correlations between bond length and local stretching force constant were observed in crystals for both the donor X-I bonds and I⋯O halogen bonds, extending for the first time the generalized Badger's rule to crystals. It is demonstrated that the halogen atom X controlling the electrostatic attraction between the σ -hole on atom I and the acceptor atom O dominates the intrinsic strength of I⋯O halogen bonds. Different oxygen-containing acceptor molecules OA and even subtle changes induced by substituents can tweak the n → σ ∗ (X-I) charge transfer character, which is the second important factor determining the I⋯O bond strength. In addition, the presence of the second halogen bond with atom X of the donor X-I bond in crystals can substantially weaken the target I⋯O halogen bond. In summary, this study performing the in situ measurement of halogen bonding strength in crystalline structures demonstrates the vast potential of the periodic local vibrational mode theory for characterizing and understanding non-covalent interactions in materials. [ABSTRACT FROM AUTHOR]

In the modeling of spin‐crossing reactions, it has become popular to directly explore the spin‐adiabatic surfaces. Specifically, through constructing spin‐adiabatic states from a two‐state Hamiltonian (with spin‐orbit coupling matrix elements) at each geometry, one can readily employ advanced geometry optimization algorithms to acquire a "transition state" structure, where the spin crossing occurs. In this work, we report the implementation of a fully‐variational spin‐adiabatic approach based on Kohn‐Sham density functional theory spin states (sharing the same set of molecular orbitals) and the Breit‐Pauli one‐electron spin‐orbit operator. For three model spin‐crossing reactions (predissociation of N2O, singlet‐triplet conversion in CH2, and CO addition to Fe(CO)4), the spin‐crossing points were obtained. Our results also indicated the Breit‐Pauli one‐electron spin‐orbit coupling can vary significantly along the reaction pathway on the spin‐adiabatic energy surface. On the other hand, due to the restriction that low‐spin and high‐spin states share the same set of molecular orbitals, the acquired spin‐adiabatic energy surface shows a cusp (ie, a first‐order discontinuity) at the crossing point, which prevents the use of standard geometry optimization algorithms to pinpoint the crossing point. An extension with this restriction removed is being developed to achieve the smoothness of spin‐adiabatic surfaces. [ABSTRACT FROM AUTHOR]

We present an RNA-As-Graphs (RAG) based inverse folding algorithm, RAG-IF , to design novel RNA sequences that fold onto target tree graph topologies. The algorithm can be used to enhance our recently reported computational design pipeline (Jain et al., NAR 2018). The RAG approach represents RNA secondary structures as tree and dual graphs, where RNA loops and helices are coarse-grained as vertices and edges, opening the usage of graph theory methods to study, predict, and design RNA structures. Our recently developed computational pipeline for design utilizes graph partitioning (RAG-3D) and atomic fragment assembly (F-RAG) to design sequences to fold onto RNA-like tree graph topologies; the atomic fragments are taken from existing RNA structures that correspond to tree subgraphs. Because F-RAG may not produce the target folds for all designs, automated mutations by RAG-IF algorithm enhance the candidate pool markedly. The crucial residues for mutation are identified by differences between the predicted and the target topology. A genetic algorithm then mutates the selected residues, and the successful sequences are optimized to retain only the minimal or essential mutations. Here we evaluate RAG-IF for 6 RNA-like topologies and generate a large pool of successful candidate sequences with a variety of minimal mutations. We find that RAG-IF adds robustness and efficiency to our RNA design pipeline, making inverse folding motivated by graph topology rather than secondary structure more productive. [ABSTRACT FROM AUTHOR]

Molecular acidity is an important physicochemical property, which is often represented by the pKa value as the measure of acidity strength. However, the accurate calculation and prediction of pKa values is still an unsolved problem for computational chemistry. In this work, we present for the first time a direct correlation between pKa values and local vibrational frequencies for 15 different groups of compounds with various substituents. This correlation was derived from a quadratic function of two selected local vibrational frequencies as independent variables used to characterize electronic structure features influencing the molecular acidity. In total, 180 molecules were investigated with this correlation model. For each group of molecules, we found a strong correlation with root mean squared errors and mean absolute errors of less than 0.11 and 0.09 pKa units, respectively. The correlation between pKa and local vibrational modes, established in this work, can be generally applied to all compounds whose pKa values are dominated by electronic substituent effects. In this regard, the new correlation model constitutes a powerful link between the well-known Hammett equation and vibrational spectroscopy. Furthermore, it allows a quick prediction of the pKa values for new group members with different substituents.pKa estimation via vibrational spectroscopy [ABSTRACT FROM AUTHOR]

Conceptually mimicking biomolecules’ ability to construct multiple‐helical aggregates with emergent properties and functions remains a long‐standing challenge. Here we report an atom‐precise 18‐copper nanocluster (NC), Cu18H(PET)14(TPP)6(NCS)3 (Cu18H) which contains a pseudo D3‐symmetrical triple‐helical Cu15 core. Structurally, Cu18H may be also viewed as sandwich type of sulfur‐bridged chiral copper cluster units [Cu6−Cu6−Cu6], endowing three‐layered 3D chirality. More importantly, the chiral NCs are aggregated into an infinite double‐stranded helix supported by intra‐strand homonuclear C−H⋅⋅⋅H−C dihydrogen contacts and inter‐strand C−H/π and C−H/S interactions. The unique multi‐layered 3D chirality and the double‐helical assembly of Cu18H are evocative of DNA. Moreover, the collective behaviours of the aggregated NCs not only exhibit crystallization‐induced emission enhancement (CIEE) and aggregation‐induced emission enhancement (AIEE) effects in the deep‐red region, but also efficiently catalyze electron transfer (ET) reaction. This study thus presents that hierarchical assemblies of atomically defined copper NCs could be intricate as observed for important biomolecules like DNA with emergent properties arising from aggregated behaviours. [ABSTRACT FROM AUTHOR]