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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[Formula: see text]–H bond and O–H bond formation with the catalytic acid, leading to an intermediate with the acid positioned over ring [Formula: see text] 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 [Formula: see text]. Then, according to URVA, breakage of the intermediate O–H bond, the formation of the new C[Formula: see text]–H bond accompanied by a double bond shift in rings [Formula: see text] and [Formula: see text] 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.

Local stretching force constants derived from periodic local vibrational modes at the vdW-DF2 density functional level have been employed to quantify the intrinsic hydrogen bond strength of 16 ice polymorphs, ices I

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.

Hydroxylation is an effective approach for the synthesis of carbon-oxygen bonds and allylic ethers. The [NHC]Au(I) catalyzed intermolecular hydroalkoxylation of allene was studied at the DFT and Coupled Cluster level of theory. Using the Unified Reaction Valley Approach (URVA), we carry out a comprehensive mechanistic analysis of [NHC]Au(I)-catalyzed and noncatalyzed reactions. The URVA study of several possible reaction pathways reveal that the [NHC]Au(I) catalyst enables the hydroalkoxylation reaction to occur via a two step mechanism based upon the Au ability to switch between π- and σ-complexation. The first step of the mechanism involves the formation of a CO bond after the transition state with no energy penalty. Following the CO bond breakage, the OH bond breaks and CH bond forms during the second step of the mechanism, as the catalyst transforms into the more stable π-Au complex. The URVA results were complemented with local vibrational mode analysis to provide measures of intrinsic bond strength for Au(I)-allene interactions of all stationary points, and NBO analysis was applied in order to observe charge transfer events along the reaction pathway. Overall, the π-Au C═C interactions of the products are stronger than those of the reactants adding to their exothermicity. Our work on the hydroxylation of allene provides new insights for the design of effective reaction pathways to produce allylic ethers and also unravels new strategies to form C-O bonds by activation of C═C bonds.

Hydride ligands of transition metal polyhydride complexes with a high coordination number are prone to fluxionality leading to interesting structural dynamics. However, the underlying polytopal rearrangement pathways have been rarely studied. Based on quantum chemical calculations carried out in this work with density functional theory and coupled-cluster theory, two new fluxional mechanisms have been identified for the rhenium polyhydride complex ReH5(PPh3)2(pyridine) to jointly account for two consecutive coalescence events in the variable-temperature NMR spectra upon heating: lateral and basal three-arm turnstile rotation. The frequently cited pseudorotation in ReH5(PPh3)2(pyridine) (Lee et al. Inorg. Chem. 1996, 35, 695) turns out to be a three-step process including two lateral three-arm turnstile steps and one basal turnstile step in between. The new fluxional mechanisms discovered in this work may also exist in other transition metal polyhydrides.

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.

A chelation-assisted selective etching (CASE) strategy is developed to construct a hierarchical polyoxometalate-based metal–organic framework (POM@MOF). The selected chelator, ethylenediaminetetraa...

A synthetic heavier p-block bismuth (Bi) complex with a rigid pincer ligand, is shown to be a Bi-based molecular electrocatalyst for proton reduction under weak acid conditions. High activity of the complex is observed in catalysis, with a icat/ip value of 95 with CH3CO2H. Experimental and theoretical studies indicate that the hydrogen evolution reaction (HER) mechanism involves generating a low-valent BiI complex and its reactivity toward acid to form a BiIII-hydride species. Subsequent protonolysis of the BiIII-hydride eliminates H2 through a heterolytic route. The HER cycling through the low-valent metal species and its hydride has been proposed previously in transition-metal (TM) centered catalysts but rarely validated in main-group catalytic systems. The finding brings insight into heavier main-group Bi-catalyzed H2 evolution and the role of low-valent main-group metal centre during catalysis.

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.

Cu is well-known to adopt a face-centered cubic (fcc) structure in the bulk phase. Ligand-stabilized Cu nanoclusters (NCs) with atomically precise structures are an emerging class of nanomaterials. However, it remains a great challenge to have non-fcc structured Cu NCs. In this contribution, we report the syntheses and total structure determination of six 28-nuclearity polyhydrido Cu NCs: [Cu28H16(dppp)4(RS)4(CF3CO2)8] (dppp = 1,3-bis(diphenylphosphino)propane, RSH = cyclohexylthiol, 1; tert-butylthiol, 3; and 2-thiophenethiol, 4) and [Cu28H16(dppe)4(RS)4(CH3CO2)6Cl2] (dppe = 1,2-bis(diphenylphosphino)ethane, RSH = (4-isopropyl)thiophenol, 2; 4-tert-butylbenzenethiol, 5; and 4-tert-butylbenzylmercaptan, 6). Their well-defined structures solved by X-ray single crystal diffraction reveal that these 28-Cu NCs are isostructural, and the overall metal framework is arranged as a sandwich structure with a core–shell Cu2@Cu16 unit held by two Cu5 fragments. One significant finding is that the organization of 18 Cu atoms in the Cu2@Cu16 could be regarded as an incomplete and distorted version of 3 × 2 × 2 “cutout” of the body-centered cubic (bcc) bulk phase, which was strikingly different to the fcc structure of bulk Cu. The bcc framework came as a surprise, as no bcc structures have been previously observed in Cu NCs. A comparison with the ideal bcc arrangement of 18 Cu atoms in the bcc lattice suggests that the distortion of the bcc structure results from the insertion of interstitial hydrides. The existence, number, and location of hydrides in these polyhydrido Cu NCs are established by combined experimental and DFT results. These results have significant implications for the development of high-nuclearity Cu hydride NCs with a non-fcc architecture.

In this work, we investigated the formation of protonated hydrogen cyanide HCNH+ and methylene amine cation CH[Formula: see text] (both identified in Titan's upper atmosphere) from three different pathways which stem from the interaction between CH4 and N+(3P). As a mechanistic tool, we used the Unified Reaction Valley Approach (URVA) complemented with the Local Mode Analysis (LMA) assessing the strength of the CN bonds formed in these reactions. Our URVA studies could provide a comprehensive overview on bond formation/cleavage processes relevant to the specific mechanism of eight reactions R1- R8 that occur across the three pathways. In addition, we could explain the formation of CH[Formula: see text] and the appearance of HCNH+ and CHNH[Formula: see text] along these paths. Although only smaller molecules are involved in these reactions including isomerization, hydrogen atom abstraction, and hydrogen molecule capture, we found a number of interesting features, such as roaming in reaction R3 or the primary interaction of H2 with the carbon atom in HCNH+ in reaction R8 followed by migration of one of the H2 hydrogen atoms to the nitrogen which is more cost effective than breaking the HH bond first; a feature often found in catalysis. In all cases, charge transfer between carbon and nitrogen could be identified as a driving force for the CN bond formation. As revealed by LMA, the CN bonds formed in reactions R1-R8 cover a broad bond strength range from very weak to very strong, with the CN bond in protonated hydrogen cyanide HCNH+ identified as the strongest of all molecules investigated in this work. Our study demonstrates the large potential of both URVA and LMA to shed new light into these extraterrestrial reactions to help better understand prebiotic processes as well as develop guidelines for future investigations involving areas of complex interstellar chemistry. In particular, the formation of CN bonds as a precursor to the extraterrestrial formation of amino acids will be the focus of future investigations. Formation of CN bonds in Titan's atmosphere visualized via the reaction path curvature.

The local vibrational mode analysis developed by Konkoli and Cremer has been successfully applied to characterize the intrinsic bond strength via local bond stretching force constants in molecular systems. A wealth of new insights into covalent bonding and weak chemical interactions ranging from hydrogen, halogen, pnicogen, and chalcogen to tetrel bonding has been obtained. In this work we extend the local vibrational mode analysis to periodic systems, i.e. crystals, allowing for the first time a quantitative in situ measure of bond strength in the extended systems of one, two, and three dimensions. We present the study of one-dimensional polyacetylene and hydrogen fluoride chains and two-dimensional layers of graphene, water, and melamine-cyanurate as well as three-dimensional ice I

Electrocatalytic hydrogen evolution reaction (HER) is a critical process in a sustainable energy conversion system. Many metal complexes as small-molecule catalysts for electrochemical H2 evolution have been reported over recent decades, which have made a great contribution to a detailed understanding of their catalytic mechanisms. In most reported mechanistic pathways, metal hydride species are always considered as key intermediates during H2 formation, with the metal centre at the active site docking both electrons and protons. These metal-centred HER routes need to employ metal ions with open coordination sites, which can accommodate multiple redox states to involve two-electron hydride transfer for H2 production. By comparison, an alternative approach, specifically focusing on redox-active ligand-centred electrocatalytic HER, has garnered increasing attention over the last six years. This review highlights recent progress in metal and metal-free ligand-centred homogeneous electrocatalytic HER since 2012 and discusses it according to two categories: organic ligand-centred and inorganic ligand-centred HER. In addition, some existing issues and suggestions for future directions in this catalytic area have been provided.

We introduce a new software, Efficient Detection of Hydrogen Bonds (EDHB), that systematically detects hydrogen bonds based on the nearest neighbors algorithm. EDHB classifies inter- and intramolecular hydrogen bonds as well as hydrogen bond networks. EDHB outperforms commonly used hydrogen bond detection methods in terms of speed of execution. An important additional feature of EDHB is that information from preceding quantum chemical studies (i.e., natural bond orbital analysis data and second energy derivative information) can be used to determine the electrostatic/covalent character of the hydrogen bonds and to calculate local-mode hydrogen bond force constants as a quantitative measure of their intrinsic strength. We applied EDHB to a diverse set of 163 proteins. We identified hydrogen bond networks forming intramolecular rings of different sizes as a common feature playing an important role for specific secondary structure orientations such as α-helixes and turns. However, these networks do not have a significant influence on the hydrogen bond strength. Our comprehensive local-mode analysis reveals the interesting result that the hydrogen bond angle is the governing factor determining the hydrogen bond strength in a protein. EDHB offers a broad range of application possibilities. In addition to proteins, EDHB can be generally used to detect and characterize hydrogen bonds in protein-ligand interactions, water clusters, and other systems where a hydrogen bond plays a critical role, as well as during molecular dynamics simulations. The program is freely available at https://github.com/ekraka/EDHB.

Hydride ligands of transition metal polyhydride complexes with a high coordination number are prone to fluxionality leading to interesting structural dynamics. However, the underlying polytopal rearrangement pathways have been rarely studied. Based on quantum chemical calculations carried out in this work with density functional theory and coupled-cluster theory, two new fluxional mechanisms have been identified for the rhenium polyhydride complex ReH

Metformin is widely used as one of the most effective first-line oral drugs for type 2 diabetes. It is difficult to be metabolized by the human body thus commonly exists in both urine and feces samples. Guanylurea is metformin’s main biotransformation product with increased concentrations in the aquatic environments. Liquid chromatography-tandem mass spectrometry (LC-MS)-based methods used for measuring the two compounds have been well developed, but extremely limited studies have tracked gas chromatography-mass spectrometry (GC-MS)-based analysis. To help better track the occurrence of the two non-volatile biguanide compounds in liquid samples, the improvement of existing GC-MS based methods for reliable metformin and guanylurea analysis is conducted. Derivatization of metformin and guanylurea is the key pretreatment procedure before the associated GC-MS analysis. Four selected factors affecting for the derivatization were evaluated, and the optimal factors include temperature (90°C), reacting time (40 min), solvent (1,4-dioxane), and ratio (1.5:1) of reagent to target component. Buformin and N-methyl-bis(trifluoroacetamide) (MBTFA) were used as the internal standard and the derivatization reagent, respectively. Calibration curves were made based on the optimal conditions of derivatization for metformin and guanylurea with the R2 values of calibration linearity achieved as 99.35% and 99.2%, respectively. The values of relative standard deviation (RSD%) of metformin and guanylurea based on seven repeated trails are 2.67% and 15.37%, respectively. The optimal conditions for enhancing the sensitization of metformin and guanylurea derivatization performance were obtained. The improved GC-MS analysis method was eventually applied for metformin and guanylurea analysis in real water samples.

The unified reaction valley approach combined with the local vibrational mode and ring puckering analysis is applied to investigate the hydrogen evolution from water in the presence of small hydrides such as BH3, metal hydrides as AlH3, and their derivatives. We studied a series of reactions involving BH3, AlH3, B2H6, Al2H6, and AlH3BH3 with one- and two-water molecules, considering multiple reaction paths. In addition, the influence of the aqueous medium was examined. A general reaction mechanism was identified for most of the reactions. Those that deviate could be associated with unusually high reaction barriers with no hydrogen release. The charge transfer along the reaction path suggests that a viable hydrogen release is achieved when the catalyst adopts the role of a charge donor during the chemical processes. The puckering analysis showed that twistboat and boat forms are the predominant configurations in the case of an intermediate six-membered ring formation, which influences the activation barrier. The local mode analysis was used as a tool to detect the H-H bond formation as well as to probe catalyst regenerability. Based on the correlation between the activation energy and the change in the charge separation for cleaving O-H and B(Al)-H bonds, two promising subsets of reactions could be identified along with prescriptions for lowering the reaction barrier individually with electron-donating/withdrawing substituents.

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.

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&ndash, H bond strengths and their change upon excitation. The natural transition orbital (NTO) analysis was used to further analyze the C=C/C&ndash, H bond strength change in excited states versus the ground state. For the first time, three excited states including &pi, y&prime, &rarr, 3s, &pi, 3py and &pi, 3pz were identified with stronger C=C ethylene double bonds than in the ground state.

Benzene and acetonitrile are two of the most commonly used solvents found in almost every chemical laboratory. Titan, Saturn’s icy moon, is one other place in the Solar system that has even larger amounts of these compounds, together with many other hydrocarbons. On Titan, organic molecules are produced in the atmosphere and carried by methane rainfall to the surface, where they either dissolve in the lakes, deposit as sandy dunes, or solidify as minerals with complex composition and structure. In order to untangle these structural complexities a reliable model of the phase behavior of these compounds at temperatures relevant to Titan is crucial. We therefore report the composition–temperature binary phase diagram of acetonitrile and benzene, and provide a detailed account of the structure and composition of the phases. This work is based on differential scanning calorimetry and in situ powder diffraction analyses with synchrotron X-ray radiation and supported by theoretical modeling. Benzene and acetonitrile were found to undergo a peritectic reaction into a cocrystal with a 1:3 acetonitrile:benzene stoichiometry. The crystal structure was solved and refined in the polar space group, R3, and the solution was confirmed and optimized by energy minimization calculations. To mimic the environment on Titan more accurately, we tested the stability of the structure under liquid ethane. The diffraction data indicate that the cocrystal undergoes further change upon contact with ethane. These results provide new insights into the structure and stability of a potential mineral on Titan, and contribute to the fundamental knowledge of some of the smallest organic molecules

11 aryl&ndash, lone pair and three aryl&ndash, anion &pi, &ndash, hole interactions are investigated, along with the argon&ndash, 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 &pi, 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 &pi, hole systems. Several factors have emerged which influence strength of the &pi, hole interactions, including aryl substituent effects, the chemical nature of atoms composing the aryl rings/ &pi, hole acceptors, and secondary bonding interactions between donors/acceptors. Substituent effects indirectly affect the &pi, hole interaction strength, where electronegative aryl-substituents moderately increase &pi, hole interaction strength. N-aryl members significantly increase &pi, hole interaction strength, and anion acceptors bind more strongly with the &pi, hole compared to charge neutral acceptors (lone&ndash, pair donors). Secondary bonding interactions between the acceptor and the atoms in the aryl ring can increase &pi, hole interaction strength, while hydrogen bonding between the &pi, hole acceptor/donor can significantly increase or decrease strength of the &pi, hole interaction depending on the directionality of hydrogen bond donation. Work is in progress expanding this research on aryl &pi, 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.

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 . Graphical abstract In this work, a PyMOL plugin named PyVibMS is developed to visualize molecular and lattice vibrations.

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

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&mdash, the Monsanto process, (ii) the Sharpless epoxidation of allylic alcohols&mdash, 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&mdash, 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.

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.

In this work a new curvilinear coordinate system is presented for the comprehensive description of polytopal rearrangements of N-coordinate compounds (N = 4-7) and systems containing an N-coordinate subunit. It is based on normal vibrational modes and a natural extension of the Cremer-Pople puckering coordinates ( J. Am. Chem. Soc. 1975, 97, 1354) together with the Zou-Izotov-Cremer deformation coordinates ( J. Phys. Chem. A 2011, 115, 8731) for ring structures to N-coordinate systems. We demonstrate that the new curvilinear coordinates are ideal reaction coordinates describing fluxional rearrangement pathways by revisiting the Berry pseudorotation and the lever mechanism in sulfur tetrafluoride, the Berry pseudorotation and two Muetterties' mechanisms in pentavalent compounds, the chimeric pseudorotation in iodine pentafluoride, Bailar and Ray-Dutt twists in hexacoordinate tris-chelates as well as the Bartell mechanism in iodine heptafluoride. The results of our study reveal that this dedicated curvilinear coordinate system can be applied to most coordination compounds opening new ways for the systematic modeling of fluxional processes.

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) {(Ag3 PO4 )8 }, reminiscent of the Ag3 PO4 photocatalyst. The SOC is capped by six interstitial sulfur atoms, giving a unique anionic cluster [Ag6 @{(Ag3 PO4 )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 @{(Ag3 PO4 )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 Ag3 PO4 , and offers a fresh template strategy for the synthesis of silver NCs with high symmetry.

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&ndash, 0.8 mdyn/&Aring, ) 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&rsquo, s rule to crystals. It is demonstrated that the halogen atom X controlling the electrostatic attraction between the &sigma, 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 &rarr, &sigma, &lowast, (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.

Photodegradation of the insecticide pymetrozine (PYM) was studied on surface of wax films, and in aqueous and nonaqueous phase. The half-life of PYM on the wax surface was approximately 250 times longer than in water. Scavenging experiments, laser flash photolysis, and spectra analysis indicated the first singlet excited state of PYM (S1 *PYM) to be the most important photoinduced species initiating the photodegradation. Quantum chemistry calculations identified significant molecular torsion and changes in the structure C–C N–N of S1 *PYM, and the absolute charges of the C N atoms increased and the bond strength weakened. Free energy surface analysis, and O18 labeling experiments further confirmed that the mechanism was two-step photoinduced hydrolysis. The first step is the hydrolysis of S1 *PYM at C N upon reaction with 2–3 water molecules (one H2O molecule as the catalyst). The second step is an intramolecular hydrogen transfer coupled with the cleavage of C–N bond and formation of two cyclic products. During the interactions, water molecules experience catalytic activation by transferring protons, while there is a negligible solvent effect. Clarifying the detailed photodegradation mechanisms of PYM is beneficial for the development of green pesticides that are photostable and effective on leaf surfaces, and photolabile and detoxified in the aquatic environment.

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 un...

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.

Theoretical studies of hydrogen-bonding based on cluster models tend to overlook the peripheral monomers which are influential. By revisiting thirteen hydrogen-bonded complexes of H2O, HF and NH3, the “push-pull” effect is identified as a general mechanism that strengthens a hydrogen bond. Enhanced Lp ( X ) → σ ∗ ( X ′ - H ) charge transfer is proved to be the core of the “push-pull” effect. The charge transfer can convert an electrostatic hydrogen bond into a covalent hydrogen bond.

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 association to Fe(CO)4], the spin-crossing points were easily 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 (i.e. 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.

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.

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.