"On-the-fly" Crystal : How to reliably and automatically characterize and construct potential energy surfaces

In this work, the Crystal  code, developed previously by the authors to find "holes" as well as legitimate transition states in existing potential energy surface (PES) functions [JPC Lett. 11, 6468 (2020)], is retooled to perform on-the-fly "direct dynamics"-type PES explorations, as well as automatic construction of new PES functions. In all of these contexts, the chief advantage of Crystal  over other methods is its ability to globally map the PES, thereby determining the most relevant regions of configuration space quickly and reliably-even when the dimensionality is rather large. Here, Crystal  is used to generate a uniformly spaced grid of density functional theory (DFT) or ab initio points, truncated over the relevant regions, which can then be used to either: (a) hone in precisely on PES features such as minima and transition states, or; (b) create a new PES function automatically, via interpolation. Proof of concept is demonstrated via application to three molecular systems: water (H2 O), (reduced-dimensional) methane (CH4 ), and methylene imine (CH2 NH).

Deep reaction network exploration of glucose pyrolysis

Resolving the reaction networks associated with biomass pyrolysis is central to understanding product selectivity and aiding catalyst design to produce more valuable products. However, even the pyrolysis network of relatively simple [Formula: see text]-D-glucose remains unresolved due to its significant complexity in terms of the depth of the network and the number of major products. Here, a transition-state-guided reaction exploration has been performed that provides complete pathways to most significant experimental pyrolysis products of [Formula: see text]-D-glucose. The resulting reaction network involves over 31,000 reactions and transition states computed at the semiempirical quantum chemistry level and approximately 7,000 kinetically relevant reactions and transition states characterized with density function theory, comprising the largest reaction network reported for biomass pyrolysis. The exploration was conducted using graph-based rules to explore the reactivities of intermediates and an adaption of the Dijkstra algorithm to identify kinetically relevant intermediates. This simple exploration policy surprisingly (re)identified pathways to most major experimental pyrolysis products, many intermediates proposed by previous computational studies, and also identified new low-barrier reaction mechanisms that resolve outstanding discrepancies between reaction pathways and yields in isotope labeling experiments. This network also provides explanatory pathways for the high yield of hydroxymethylfurfural and the reaction pathway that contributes most to the formation of hydroxyacetaldehyde during glucose pyrolysis. Due to the limited domain knowledge required to generate this network, this approach should also be transferable to other complex reaction network prediction problems in biomass pyrolysis.

The Adsorption Mechanism of Hydrogen on FeO Crystal Surfaces: A Density Functional Theory Study

The hydrogen-based direct reduction of iron ores is a disruptive routine used to mitigate the large amount of CO₂ emissions produced by the steel industry. The reduction of iron oxides by H₂ involves a variety of physicochemical phenomena from macroscopic to atomistic scales. Particularly at the atomistic scale, the underlying mechanisms of the interaction of hydrogen and iron oxides is not yet fully understood. In this study, density functional theory (DFT) was employed to investigate the adsorption behavior of hydrogen atoms and H₂ on different crystal FeO surfaces to gain a fundamental understanding of the associated interfacial adsorption mechanisms. It was found that H₂ molecules tend to be physically adsorbed on the top site of Fe atoms, while Fe atoms on the FeO surface act as active sites to catalyze H₂ dissociation. The dissociated H atoms were found to prefer to be chemically bonded with surface O atoms. These results provide a new insight into the catalytic effect of the studied FeO surfaces, by showing that both Fe (catalytic site) and O (binding site) atoms contribute to the interaction between H₂ and FeO surfaces.

Constant advance replicas method for locating minimum energy paths and transition states

The chain-of-states (CoS) constant advance replicas (CAR) method and its climbing image variant (CI-CAR) for locating minimum energy paths (MEPs) and transition states are reported. The CAR algorithm applies the Lagrange multiplier method for imposing holonomic constraints on a chain-of-replicas, aiming to maintain equal mass-weighted/scaled root-mean-square (RMS) distances between the adjacent replicas by removing the sliding-down displacements contributed by the potential gradients during path optimization. Two contextual regularization schemes with clear geometrical interpretations are implemented to jointly promote high convergence and numerical robustness of the CAR algorithm. We show that the constrained reaction path can be solved normally within 5 steps of Lagrange multiplier updates with remarkably high numerical precision via the CAR approach. The efficacy of the CAR methods is demonstrated by testing on multiple analytical, classical, and quantum mechanical transition paths: the Müller potential, the alanine dipeptide isomerization, the helix unwinding of the VIVITLVMLKKK 12-mer peptide, and the Baker set of reactions. We also explore the potential of applying adaptive momentum (AdaM) optimizers for locating optimal transition paths under complex conformational changes. Most importantly, we discuss extensively the differences and connections between our newly proposed CAR methods and several related methods, with focuses on the reaction path with holonomic constraints (RPCons) approach of Brokaw et al. [J. Chem. Theory Comput. 2009, 5 (8), 2050-2061] and the state-of-the-art string method (SM) of E et al. [J. Chem. Phys. 2007, 126 (16), 164103]. The CAR approach represents a latest update to the general theoretical framework of reaction path finding algorithms in the two-ended CoS regime.

Energetics and mechanisms for decomposition of cationized amino acids and peptides explored using guided ion beam tandem mass spectrometry

Fragmentation studies of cationized amino acids and small peptides as studied using guided ion beam tandem mass spectrometry (GIBMS) are reviewed. After a brief examination of the key attributes of the GIBMS approach, results for a variety of systems are examined, compared, and contrasted. Cationization of amino acids, diglycine, and triglycine with alkali cations generally leads to dissociations in which the intact biomolecule is lost. Exceptions include most lithiated species as well as a few examples for sodiated and one example for potassiated species. Like the lithiated species, cationization by protons leads to numerous dissociation channels. Results for protonated glycine, cysteine, asparagine, diglycine, and a series of tripeptides are reviewed, along with the thermodynamic consequences that can be gleaned. Finally, the important physiological process of the deamidation of asparagine (Asn) residues is explored by the comparison of five dipeptides in which the C-terminal partner (AsnXxx) is altered. The GIBMS thermochemistry is shown to correlate well with kinetic results from solution phase studies.

Deciphering the Differences in Ambident Reactivity between the Cyanate, Thiocyanate Ions, and their P- and As-Containing Analogues

Although the cyanate and thiocyanate anions belong to the most known textbook examples of ambident nucleophiles, the electronic factors that determine their markedly differing reactivities are still unclear. Their recently discovered P- and As-containing [PCX]- and [AsCX]-analogues (X: O, S, Se), whose ambident nature is practically unexplored, may serve as ideal basis for comparison to clarify these differences. Herein we present comprehensive theoretical investigations on the nucleophilic behaviours of the whole set of so far known [ECX]-(E: N, P, As, X: O, S, Se) anions, aiming for a systematic understanding of the reactivity patterns and deciphering the factors that govern the nucleophilic substitutions. Our results indicate that the SN2 reactions of the O-containing [ECO]- ions are thermodynamically preferred at the E pnictogen centres, while the kinetic contributions are only substantial for the N-containing [NCX]-anions. The ambident reactivities of the congeners that contain N or O significantly differ from those with P, As, S, or Se heteroatoms, in line with the inert s-orbital effect, characteristic for the heavier elements. By analysing the electronic structures and bonding patterns of the anions and relevant transition state structures, we offer clear explanations for the differing reactivities of the whole set of [ECX]-anions.

Chiral explosives: A theoretical investigation of structure and chiroptical properties of triacetone triperoxide and hexamethylene triperoxide diamine

Triacetone triperoxide (TATP) and hexamethylene triperoxide diamine (HMTD) are cyclic peroxides that exhibit atropisomerism resulting from restricted rotation around three peroxide bonds. As a result, one pair of enantiomers with D₃ symmetry and another pair of enantiomers with C₂ symmetry can be identified. Previous studies, based on mass spectrometry data and computational results, have shown that conformations of TATP with D₃ and C₂ symmetry can be isolated. Assuming that enantiomer samples of TATP and HMTD can be obtained with sufficient enantiopurity, we investigated their chiroptical properties, namely, optical rotatory dispersion (ORD), vibrational circular dichroism (VCD), and Raman optical activity (VROA). ORD curves and VCD spectra are seen to be very similar for D₃ - and C₂ -symmetric atropisomers with the same overall helicity. Predicted VROA results, however, show significant differences between D₃ - and C₂ -symmetric atropisomers with the same overall helicity. The D₃ -symmetric atropisomer is predicted to exhibit considerably larger magnitude vibrational optical activity signals than the C₂ -symmetric atropisomer.

Transcriptional networks of transient cell states during human prefrontal cortex development

The human brain is divided into various anatomical regions that control and coordinate unique functions. The prefrontal cortex (PFC) is a large brain region that comprises a range of neuronal and non-neuronal cell types, sharing extensive interconnections with subcortical areas, and plays a critical role in cognition and memory. A timely appearance of distinct cell types through embryonic development is crucial for an anatomically perfect and functional brain. Direct tracing of cell fate development in the human brain is not possible, but single-cell transcriptome sequencing (scRNA-seq) datasets provide the opportunity to dissect cellular heterogeneity and its molecular regulators. Here, using scRNA-seq data of human PFC from fetal stages, we elucidate distinct transient cell states during PFC development and their underlying gene regulatory circuitry. We further identified that distinct intermediate cell states consist of specific gene regulatory modules essential to reach terminal fate using discrete developmental paths. Moreover, using in silico gene knock-out and over-expression analysis, we validated crucial gene regulatory components during the lineage specification of oligodendrocyte progenitor cells. Our study illustrates unique intermediate states and specific gene interaction networks that warrant further investigation for their functional contribution to typical brain development and discusses how this knowledge can be harvested for therapeutic intervention in challenging neurodevelopmental disorders.

An automated method for graph-based chemical space exploration and transition state finding

Algorithms that automatically explore the chemical space have been limited to chemical systems with a low number of atoms due to expensive involved quantum calculations and the large amount of possible reaction pathways. The method described here presents a novel solution to the problem of chemical exploration by generating reaction networks with heuristics based on chemical theory. First, a second version of the reaction network is determined through molecular graph transformations acting upon functional groups of the reacting. Only transformations that break two chemical bonds and form two new ones are considered, leading to a significant performance enhancement compared to previously presented algorithm. Second, energy barriers for this reaction network are estimated through quantum chemical calculations by a growing string method, which can also identify non-octet species missed during the previous step and further define the reaction network. The proposed algorithm has been successfully applied to five different chemical reactions, in all cases identifying the most important reaction pathways.

Efficient and Accurate Description of Diels-Alder Reactions Using Density Functional Theory

Modeling chemical reactions using Quantum Chemistry is a widely used predictive strategy capable to complement experiments in order to understand the intrinsic mechanisms guiding the chemicals towards the most favorable reaction products. However, at this purpose, it is mandatory to use reliable and computationally tractable theoretical methods. In this work, we focus on six Diels-Alder reactions of increasing complexity and perform an extensive benchmark of middle- to low-cost computational approaches to predict the characteristic reactions energy barriers. We found that Density Functional Theory, using the ωB97XD, LC-ωPBE, CAM-B3LYP, M11 and MN12SX functionals, with empirical dispersion corrections coupled to an affordable 6-31G basis set, provides quality results for this class of reactions, at a small computational effort. Such efficient and reliable simulation protocol opens perspectives for hybrid QM/MM molecular dynamics simulations of Diels-Alder reactions including explicit solvation.

Transition States in Single-Case Experimental Designs: A Retrospective Consecutive-Controlled Case Series Investigation

Behavioral interventions to decrease problem behavior often involve the use of single-case experimental designs in which an individual's responding during a treatment condition is compared to responding during a control or baseline condition. It is possible that during the initial introduction of treatment, problem behavior continues to occur at baseline rates before behavior reduction is observed; this phenomenon is called a transition state. Evaluated the prevalence of transition states in the Journal of Applied Behavior Analysis and found that they occurred within 5.3% of the published literature. The current study replicated and extended Brogan et al. by evaluating the prevalence of transition states in unpublished clinical data of patients admitted to an inpatient hospital for the treatment of severe problem behavior. Using a retrospective consecutive-controlled case series, transition states were observed in 3% of cases for an average duration of 4.8 sessions. We discuss factors that may affect transitional behavior between phases and relevant implications for practice and research.

Search for transition states with external forces

It is much more difficult to find on the potential energy surface (PES) a transition state (TS) than a local minimum (LM). We propose a new methodology which makes this task much easier. Applying external forces to nuclei in a molecule we can locate on PES not just one particular TS but a number of consecutive transition states. With our approach it is possible to move over PES from one transition state to another without involving any local minima. The latter can be located in a separate step through the reaction path calculations performed for every transition state found before. Preliminary results for the 2-fluorofuran molecule illustrate the usefulness of the proposed method.

Observing the base-by-base search for native structure along transition paths during the folding of single nucleic acid hairpins

Biomolecular folding involves searching among myriad possibilities for the native conformation, but the elementary steps expected from theory for this search have never been detected directly. We probed the dynamics of folding at high resolution using optical tweezers, measuring individual trajectories as nucleic acid hairpins passed through the high-energy transition states that dominate kinetics and define folding mechanisms. We observed brief but ubiquitous pauses in the transition states, with a dwell time distribution that matched microscopic theories of folding quantitatively. The sequence dependence suggested that pauses were dominated by microbarriers from nonnative conformations during the search by each nucleotide residue for the native base-pairing conformation. Furthermore, the pauses were position dependent, revealing subtle local variations in energy-landscape roughness and allowing the diffusion coefficient describing the microscopic dynamics within the barrier to be found without reconstructing the shape of the energy landscape. These results show how high-resolution measurements can elucidate key microscopic events during folding to test fundamental theories of folding.

Bispericyclic Diels-Alder Dimerization of ortho-Quinols in Natural Product (Bio)Synthesis: Bioinspired Chemical 6-Step Synthesis of (+)-Maytenone

Many natural products of plant or microbial origins are derived from enzymatic dearomative oxygenation of 2-alkylphenolic precursors into 6-alkyl-6-hydroxycyclohexa-2,4-dienones. These so-called ortho-quinols cyclodimerize via a remarkably selective bispericyclic Diels-Alder reaction. Whether or not the intervention of catalytic or dirigent proteins is involved during this final step of the biosynthesis of these natural products, this cyclodimerization of ortho-quinols can be chemically reproduced in the laboratory with the same strict level of site-specific regioselectivity and stereoselectivity. This unique yet unified process, which finds its rationale in the inherent chemical reactivity of those ortho-quinols, is illustrated herein by an efficient and bioinspired first chemical synthesis of one of the most structurally complex and synthetically challenging examples of such natural cyclodimers, the bisditerpenoid (+)-maytenone.

Interconnectivity between Surface Reactivity and Self-Assembly of Kemp Elimination Catalyzing Nanorods

Understanding the fundamental facts behind dynamicity of catalytic processes has been a longstanding quest across disciplines. Herein, we report self-assembly of catalytically active gold nanorods that can be regulated by tuning its reactivity towards a proton transfer reaction at different pH. Unlike substrate-induced templating and co-operativity, the enhanced aggregation rate is due to alteration of catalytic surface charge only during reactivity as negatively charged transition state of reactant (5-nitrobenzisoxazole) is formed on positively charged nanorod while undergoing a concerted E2-pathway. Herein, enhanced diffusivity during catalytic processes might also act as an additional contributing factor. Furthermore, we have also shown that nanosized hydrophobic cavities of clustered nanorods can also efficiently accelerate the rate of an aromatic nucleophilic substitution reaction, which also demonstrates a catalytic phenomenon that can lead to cascading of other reactions where substrates and products of the starting reactions are not directly involved.

Bromination Mechanism of closo-1,2-C2 B10 H12 and the Structure of the Resulting 9-Br-closo-1,2-C2 B10 H11 Determined by Gas Electron Diffraction

9-Br-closo-1,2-C₂ B₁₀ H₁₁ has been prepared and its gas-phase structure has been examined by means of gas electron diffraction. The structure of the carbaborane core is similar to the structure of the parent compound, which is of C_2v symmetry. A DFT-based search for the corresponding reaction pathway of the bromination of closo-1,2-C₂ B₁₀ H₁₂ revealed that the catalytic amount of aluminum reduces the barrier of the initial attack of the bromination agent toward the negatively charged part of the icosahedral carbaborane, i. e., the first transition state, from about 40 to about 27 kcalmol^-1 . The Br-Br bond is weakened by an intermediate binding to the large π-hole on the aluminum atom of AlBr₃ , which is the driving force for the AlBr₃ -catalyzed bromination.

On the Crucial Role of Isolated Electronic States in the Thermal Reaction of ReC+ with Dihydrogen

Presented here is that isolated, long‐lived electronic states of ReC⁺ serve as the root cause for distinctly different reactivities of this diatomic ion in the thermal activation of dihydrogen. Detailed high‐level quantum chemical calculations support the experimental findings obtained in the highly diluted gas phase using FT‐ICR mass spectrometry. The origin for the existence of these long‐lived excited electronic states and the resulting implications for the varying mechanisms of dihydrogen splitting are addressed.

scRCMF: Identification of Cell Subpopulations and Transition States From Single-Cell Transcriptomes

Single cell technologies provide an unprecedented opportunity to explore the heterogeneity in a biological process at the level of single cells. One major challenge in analyzing single cell data is to identify cell subpopulations, stable cell states, and cells in transition between states. To elucidate the transition mechanisms in cell fate dynamics, it is highly desirable to quantitatively characterize cellular states and intermediate states. Here, we present scRCMF, an unsupervised method that identifies stable cell states and transition cells by adopting a nonlinear optimization model that infers the latent substructures from a gene-cell matrix. We incorporate a random coefficient matrix-based regularization into the standard nonnegative matrix decomposition model to improve the reliability and stability of estimating latent substructures. To quantify the transition capability of each cell, we propose two new measures: single-cell transition entropy (scEntropy) and transition probability (scTP). When applied to two simulated and three published scRNA-seq datasets, scRCMF not only successfully captures multiple subpopulations and transition processes in large-scale data, but also identifies transition states and some known marker genes associated with cell state transitions and subpopulations. Furthermore, the quantity scEntropy is found to be significantly higher for transition cells than other cellular states during the global differentiation, and the scTP predicts the "fate decisions" of transition cells within the transition. The present study provides new insights into transition events during differentiation and development.

Further discussion on the reaction behaviour of triallyl isocyanurate in the UV radiation cross-linking process of polyethylene: a theoretical study

Further theoretical investigation on the reaction behaviour of triallyl isocyanurate (TAIC) in the UV radiation cross-linking process of polyethylene (PE) is accomplished by density functional theory for high voltage cable insulation materials. The reaction potential energy information of the 13 reaction channels at B3LYP/6-311 + G(d,p) level are identified. These have been explored that the TAIC take part in the reaction behaviour on ground state during UV radiation cross-linking process and TAIC intra-molecular isomerization reaction itself. In addition, the results show that the effect of multiplication and acceleration for the cross-linking reaction of trimethylopropane trimethacrylate (TMPTMA) would be better than that of TAIC. It has further clarified the reasons why UV radiation cross-linking reaction of PE had been initiated by benzophenone (Bp), and the TAIC or TMPTMA needed to take part. The results obtained in the present study could directly guide both the optimization of UV radiation cross-linking PE process and the development of the insulation material of high-voltage cable in real application.

Design of Chiral Bifunctional Dialkyl Sulfide Catalysts for Regio-, Diastereo-, and Enantioselective Bromolactonization

Although a wide variety of chiral organocatalysts have been developed for asymmetric transformations, effective chiral dialkyl sulfide organocatalysts remain relatively rare and under-developed, despite the potential utility of dialkyl sulfide catalysts. Herein, we report the development of chiral bifunctional dialkyl sulfide catalysts possessing a urea moiety for regio-, diastereo-, and enantioselective bromolactonization. The importance of the bifunctional design of chiral sulfide catalysts was clearly demonstrated in the present work. The roles of both the sulfide and urea moieties of the catalyst were clarified based on the results of experimental and theoretical investigation.

Nucleophilic Influences and Origin of the SN 2 Allylic Effect

The potential energy surfaces for the S_N 2 reactions of allyl and propyl chlorides with 21 anionic and neutral nucleophiles was studied by using ωB97X-D/6-311++G(3df,2pd) computations. The "allylic effect" on S_N 2 barriers was observed for all reactions, and compared with propyl substrates, the energy barriers differed by -0.2 to -4.5 kcal mol^-1 in the gas phase. Strong correlations of the S_N 2 net activation barriers with cation affinities, proton affinities, and electrostatic potentials at nuclei demonstrated the powerful influence of electrostatic interactions on these reactions. For the reactions of anionic (but not neutral) nucleophiles with allyl chloride, some of the incoming negative charge (0.2-18 %) migrated into the carbon chains, which would provide secondary stabilization of the S_N 2 transition states. Activation strain analysis provided additional insight into the allylic effect by showing that the energy of geometric distortion for the reactants to reach the S_N 2 transition state was smaller for each allylic reaction than for its propyl analogue. In many cases, the interaction energies between the substrate and nucleophile in this analysis were more favorable for propyl chloride reactions, but this compensation did not overcome the predominant strain energy effect.

Analyzing Reaction Rates with the Distortion/Interaction-Activation Strain Model

The activation strain or distortion/interaction model is a tool to analyze activation barriers that determine reaction rates. For bimolecular reactions, the activation energies are the sum of the energies to distort the reactants into geometries they have in transition states plus the interaction energies between the two distorted molecules. The energy required to distort the molecules is called the activation strain or distortion energy. This energy is the principal contributor to the activation barrier. The transition state occurs when this activation strain is overcome by the stabilizing interaction energy. Following the changes in these energies along the reaction coordinate gives insights into the factors controlling reactivity. This model has been applied to reactions of all types in both organic and inorganic chemistry, including substitutions and eliminations, cycloadditions, and several types of organometallic reactions.

Review: The ATPase mechanism of myosin and actomyosin

Myosins are a large family of molecular motors that use the common P-loop, Switch 1 and Switch 2 nucleotide binding motifs to recognize ATP, to create a catalytic site than can efficiently hydrolyze ATP and to communicate the state of the nucleotide pocket to other allosteric binding sites on myosin. The energy of ATP hydrolysis is used to do work against an external load. In this short review I will outline current thinking on the mechanism of ATP hydrolysis and how the energy of ATP hydrolysis is coupled to a series of protein conformational changes that allow a myosin, with the cytoskeleton track actin, to operate as a molecular motor of distinct types; fast movers, processive motors or strain sensors. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 483-491, 2016.

Reliable and efficient reaction path and transition state finding for surface reactions with the growing string method

The computational challenge of fast and reliable transition state and reaction path optimization requires new methodological strategies to maintain low cost, high accuracy, and systematic searching capabilities. The growing string method using internal coordinates has proven to be highly effective for the study of molecular, gas phase reactions, but difficulties in choosing a suitable coordinate system for periodic systems has prevented its use for surface chemistry. New developments are therefore needed, and presented herein, to handle surface reactions which include atoms with large coordination numbers that cannot be treated using standard internal coordinates. The double-ended and single-ended growing string methods are implemented using a hybrid coordinate system, then benchmarked for a test set of 43 elementary reactions occurring on surfaces. These results show that the growing string method is at least 45% faster than the widely used climbing image-nudged elastic band method, which also fails to converge in several of the test cases. Additionally, the surface growing string method has a unique single-ended search method which can move outward from an initial structure to find the intermediates, transition states, and reaction paths simultaneously. This powerful explorative feature of single ended-growing string method is demonstrated to uncover, for the first time, the mechanism for atomic layer deposition of TiN on Cu(111) surface. This reaction is found to proceed through multiple hydrogen-transfer and ligand-exchange events, while formation of H-bonds stabilizes intermediates of the reaction. Purging gaseous products out of the reaction environment is the driving force for these reactions. © 2017 Wiley Periodicals, Inc.

Dynamical Bifurcation in Gas-Phase XH- + CH3 Y SN 2 Reactions: The Role of Energy Flow and Redistribution in Avoiding the Minimum Energy Path

The gas-phase reactions of XH^- (X=O, S) + CH₃ Y (Y=F, Cl, Br) span nearly the whole range of S_N 2 pathways, and show an intrinsic reaction coordinate (IRC) (minimum energy path) with a deep well owing to the CH₃ XH⋅⋅⋅Y^- (or CH₃ S^- ⋅⋅⋅HF) hydrogen-bonded postreaction complex. MP2 quasiclassical-type direct dynamics starting at the [HX⋅⋅⋅CH₃ ⋅⋅⋅Y]^- transition-state (TS) structure reveal distinct mechanistic behaviors. Trajectories that yield the separated CH₃ XH+Y^- (or CH₃ S^- +HF) products directly are non-IRC, whereas those that sample the CH₃ XH⋅⋅⋅Y^- (or CH₃ S^- ⋅⋅⋅HF) complex are IRC. The IRCIRC/non-IRC ratios of 90:10, 40:60, 25:75, 2:98, 0:100, and 0:100 are obtained for (X, Y)=(S, F), (O, F), (S, Cl), (S, Br), (O, Cl), and (O, Br), respectively. The properties of the energy profiles after the TS cannot provide a rationalization of these results. Analysis of the energy flow in dynamics shows that the trajectories cross a dynamical bifurcation, and that the inability to follow the minimum energy path arises from long vibration periods of the X-C⋅⋅⋅Y bending mode. The partition of the available energy to the products into vibrational, rotational, and translational energies reveals that if the vibrational contribution is more than 80 %, non-IRC behavior dominates, unless the relative fraction of the rotational and translational components is similar, in which case a richer dynamical mechanism is shown, with an IRC/non-IRC ratio that correlates to this relative fraction.

Duality of Orbital-Symmetry-Allowed Transition States for Thermal Sigmatropic Hydrogen Shifts in Transition Metal Compounds

Herein, the Zimmerman Möbius/Hückel concept is extended to pericyclic reactions involving transition metals. While sigmatropic hydrogen shifts in parent hydrocarbons are either uniquely antarafacial or suprafacial, we have shown by theoretical orbital topology considerations and quantum chemical computations at DFT level that both modes of stereoselectivity must become allowed in the same system as a consequence of Craig-Möbius-type orbital arrays, in which a transition metal d orbital induces a phase dislocation in metallacycles. This may have fundamental implications for the understanding of reactivity and bonding in organometallic chemistry.

Modeling a halogen dance reaction mechanism: A density functional theory study

Since the discovery of the halogen dance (HD) reaction more than 60 years ago, numerous insights into the mechanism have been unveiled. To date however, the reaction has not been investigated from a theoretical perspective. Density functional theory (DFT) was used to model the potential energy surface linking the starting reagents to the lithiated products for each step in the mechanism using a thiophene substrate. It was found that the lithium-halogen exchange mechanism is critical to understand the HD mechanism in detail and yielded the knowledge that SN 2 transition states (TS) are favored over the four-center type for the lithium-bromine exchange steps. The overall driving force for the HD is thermodynamics, while the kinetic factors tightly control the reaction path through temperature. The SN 2 lithium-bromide TS are barrierless, except the second, which is the limiting step. Finally, the model for the HD is discovered to be a pseudo-clock type, due to a highly favorable bromide catalysis step and the reformation of 2-bromothiophene. © 2016 Wiley Periodicals, Inc.

Ab Initio Calculation of Rate Constants for Molecule-Surface Reactions with Chemical Accuracy

The ab initio prediction of reaction rate constants for systems with hundreds of atoms with an accuracy that is comparable to experiment is a challenge for computational quantum chemistry. We present a divide-and-conquer strategy that departs from the potential energy surfaces obtained by standard density functional theory with inclusion of dispersion. The energies of the reactant and transition structures are refined by wavefunction-type calculations for the reaction site. Thermal effects and entropies are calculated from vibrational partition functions, and the anharmonic frequencies are calculated separately for each vibrational mode. This method is applied to a key reaction of an industrially relevant catalytic process, the methylation of small alkenes over zeolites. The calculated reaction rate constants (free energies), pre-exponential factors (entropies), and enthalpy barriers show that our computational strategy yields results that agree with experiment within chemical accuracy limits (less than one order of magnitude).

Ion-Pair SN 2 Substitution: Activation Strain Analyses of Counter-Ion and Solvent Effects

The ion-pair SN 2 reactions of model systems MnF(n-1) +CH3Cl(M(+) =Li(+), Na(+), K(+), and MgCl(+); n=0, 1) have been quantum chemically explored by using DFT at the OLYP/6-31++G(d,p) level. The purpose of this study is threefold: 1) to elucidate how the counterion M(+) modifies ion-pair SN 2 reactivity relative to the parent reaction F(-) +CH3Cl; 2) to determine how this influences stereochemical competition between the backside and frontside attacks; and 3) to examine the effect of solvation on these ion-pair SN2 pathways. Trends in reactivity are analyzed and explained by using the activation strain model (ASM) of chemical reactivity. The ASM has been extended to treat reactivity in solution. These findings contribute to a more rational design of tailor-made substitution reactions.

Direct Staudinger-Phosphonite Reaction Provides Methylphosphonamidates as Inhibitors of CE4 De-N-acetylases

De-N-acetylases of β-(1→6)-D-N-acetylglucosamine polymers (PNAG) and β-(1→4)-D-N-acetylglucosamine residues in peptidoglycan are attractive targets for antimicrobial agents. PNAG de-N-acetylases are necessary for biofilm formation in numerous pathogenic bacteria. Peptidoglycan de-N-acetylation facilitates bacterial evasion of innate immune defenses. To target these enzymes, transition-state analogue inhibitors containing a methylphosphonamidate have been synthesized through a direct Staudinger-phosphonite reaction. The inhibitors were tested on purified PgaB, a PNAG de-N-acetylase from Escherichia coli, and PgdA, a peptidoglycan de-N-acetylase from Streptococcus pneumonia. Herein, we describe the most potent inhibitor of peptidoglycan de-N-acetylases reported to date (Ki =80 μM). The minimal inhibition of PgaB observed provides insight into key structural and functional differences in these enzymes that will need to be considered during the development of future inhibitors.

Tuning the electronic coupling in cyclometalated diruthenium complexes through substituent effects: a correlation between the experimental and calculated results

A common bridging ligand, 3,3',5,5'-tetrakis(N-methylbenzimidazol-2-yl)biphenyl, and four terpyridine terminal ligands with various substituents (amine, tolyl, nitro, and ester groups) have been used to synthesize ten cyclometalated diruthenium complexes 1(2+) -10(2+) . Among them, compounds 1(2+) -6(2+) are redox nonsymmetric, and others are symmetric. These complexes show two Ru(III/II) processes and an intervalence charge transfer (IVCT) transition in the one-electron oxidized state. The potential separation (ΔE) of 1(2+) -10(2+) has been correlated to the energy difference ΔG(0) , the energy of the IVCT band Eop , and the ground-state delocalization coefficient α(2) . Time-dependent (TD)DFT calculations suggest that the absorptions in the visible region of 1(2+) -6(2+) are mainly associated with the metal-to-ligand charge-transfer transitions from both ruthenium ions and to both terminal ligands and the bridging ligand. However, the energies of these transitions vary significantly. DFT calculations have been performed on 1(2+) -6(2+) and 1(3+) -6(3+) to give information on the electronic structures and spin populations of the mixed-valent compounds. The TDDFT-predicted IVCT excitations reproduce well the experimental trends in transition energies. In addition, three monoruthenium complexes have been synthesized for a comparison study.

Substrate dependent reaction channels of the Wolff-Kishner reduction reaction: A theoretical study

Wolff–Kishner reduction reactions were investigated by DFT calculations for the first time. B3LYP/6-311+G(d,p) SCRF=(PCM, solvent = 1,2-ethanediol) optimizations were carried out. To investigate the role of the base catalyst, the base-free reaction was examined by the use of acetone, hydrazine (H₂N–NH₂) and (H₂O)₈. A ready reaction channel of acetone → acetone hydrazine (Me₂C=N–NH₂) was obtained. The channel involves two likely proton-transfer routes. However, it was found that the base-free reaction was unlikely at the N₂ extrusion step from the isopropyl diimine intermediate (Me₂C(H)–N=N–H). Two base-catalyzed reactions were investigated by models of the ketone, H₂N–NH₂ and OH⁻(H₂O)₇. Here, ketones are acetone and acetophenone. While routes of the ketone → hydrazone → diimine are similar, those from the diimines are different. From the isopropyl diimine, the N₂ extrusion and the C–H bond formation takes place concomitantly. The concomitance leads to the propane product concertedly. From the (1-phenyl)ethyl substituted diimine, a carbanion intermediate is formed. The para carbon of the phenyl ring of the anion is subject to the protonation, which leads to a 3-ethylidene-1,4-cyclohexadiene intermediate. Its [1,5]-hydrogen migration gives the ethylbenzene product. For both ketone substrates, the diimines undergoing E2 reactions were found to be key intermediates.

Ene-ene-yne reactions: activation strain analysis and the role of aromaticity

The trend in reactivity of the thermal cycloisomerization reactions of 1,3-hexadien-5-ynes, A=B-C=D-E≡F, were explored and analyzed by using density functional theory at the M06-2X/def2-TZVPP level. These reactions proceed through formally aromatic transition states to form a bent-allene intermediate with relatively high activation barriers. Activation-strain analyses show that the major factor controlling this Hopf cyclization is the geometrical strain energy associated with the rotation of the terminal [A] group. This rotation is necessary for achieving a favorable HOMO-LUMO overlap with the yne-moiety [F] associated with the formation of the new A-F single bond. In addition, the relationship between the aromaticity of the corresponding cyclic transition states (all six-membered rings) and the computed activation barriers were analyzed. The calculations also indicate that the aromatization of the bent-allene structures takes place through two consecutive 1,2-hydrogen shifts, the second one exhibiting negligible energy barriers.

Attacking mechanism of hydroxyl radical to DNA base-pair: density functional study in vacuum and in water

Recently, the influence of radiation on human body has been recognized as a serious problem. In particular, highly reactive hydroxyl radicals *OH produced by the radiation react with DNA, resulting in a great damage on its structure and electronic properties. It is thus important to investigate the reaction mechanism of *OH to DNA for elucidating the initial damage in DNA induced by the radiation. In the present study, we search for transition states (TS) of the reaction between G-C/A-T base-pair and [Formula: see text] in vacuum and in water, by the density functional theory (DFT) calculations. At first, we obtain the stable structures for the dehydrogenated G-C and A-T, in which the hydrogen atom of NH2 group of G or A base is abstracted by [Formula: see text]. From the structures of the dehydrogenated as well as the natural base-pairs, the TS between these structures is searched for and the activation free energy (AFE) is estimated for the reaction. In vacuum, AFEs for the G-C and A-T are almost the same each other, while the stabilization energy by the reaction for G-C is about 4.9 kcal/mol larger than that for A-T, indicating that the population of the dehydrogenated G-C is remarkably larger than that of the dehydrogenated A-T in vacuum. On the other hand, in water approximated by the continuum solvation model, the AFE for A-T is 2.6 kcal/mol smaller than that for G-C, indicating that the reaction dehydrogenated by [Formula: see text] occurs more frequently for the solvated A-T base-pair than G-C.

Combined inhibitor free-energy landscape and structural analysis reports on the mannosidase conformational coordinate

Mannosidases catalyze the hydrolysis of a diverse range of polysaccharides and glycoconjugates, and the various sequence-based mannosidase families have evolved ingenious strategies to overcome the stereoelectronic challenges of mannoside chemistry. Using a combination of computational chemistry, inhibitor design and synthesis, and X-ray crystallography of inhibitor/enzyme complexes, it is demonstrated that mannoimidazole-type inhibitors are energetically poised to report faithfully on mannosidase transition-state conformation, and provide direct evidence for the conformational itinerary used by diverse mannosidases, including β-mannanases from families GH26 and GH113. Isofagomine-type inhibitors are poor mimics of transition-state conformation, owing to the high energy barriers that must be crossed to attain mechanistically relevant conformations, however, these sugar-shaped heterocycles allow the acquisition of ternary complexes that span the active site, thus providing valuable insight into active-site residues involved in substrate recognition.

An aniline dication-like transition state in the Bamberger rearrangement

A Bamberger rearrangement of N-phenylhydroxylamine, Ph–N(OH)H, to p-aminophenol was investigated by DFT calculations for the first time. The nitrenium ion, C₆H₅–NH⁺, suggested and seemingly established as an intermediate was calculated to be absent owing to the high nucleophilicity of the water cluster around it. First, a reaction of the monoprotonated system, Ph–N(OH)H + H₃O⁺(H₂O)_n (n = 4 and 14) was examined. However, the rate-determining transition states involving proton transfers were calculated to have much larger activation energies than the experimental one. Second, a reaction of the diprotonated system, Ph–N(OH)H + (H₃O⁺)₂(H₂O)₁₃, was traced. An activation energy similar to the experimental one was obtained. A new mechanism of the rearrangement including the aniline dication-like transition state was proposed.

Free energy landscape for the binding process of Huperzine A to acetylcholinesterase

Drug-target residence time (t = 1/k(off), where k(off) is the dissociation rate constant) has become an important index in discovering better- or best-in-class drugs. However, little effort has been dedicated to developing computational methods that can accurately predict this kinetic parameter or related parameters, k(off) and activation free energy of dissociation (ΔG(off)≠). In this paper, energy landscape theory that has been developed to understand protein folding and function is extended to develop a generally applicable computational framework that is able to construct a complete ligand-target binding free energy landscape. This enables both the binding affinity and the binding kinetics to be accurately estimated. We applied this method to simulate the binding event of the anti-Alzheimer's disease drug (-)-Huperzine A to its target acetylcholinesterase (AChE). The computational results are in excellent agreement with our concurrent experimental measurements. All of the predicted values of binding free energy and activation free energies of association and dissociation deviate from the experimental data only by less than 1 kcal/mol. The method also provides atomic resolution information for the (-)-Huperzine A binding pathway, which may be useful in designing more potent AChE inhibitors. We expect this methodology to be widely applicable to drug discovery and development.

Presence or absence of a novel charge-transfer complex in the base-catalyzed hydrolysis of N-ethylbenzamide or ethyl benzoate

Reaction paths of base-catalyzed hydrolyses of isoelectronic substrates, Ph–C(=O)–X–Et [X = O (ethyl benzoate) and X = NH (N-ethylbenzamide)], were traced by DFT calculations. To simulate bond interchanges accompanied by proton transfers, a cluster model of Ph–C(=O)–X–Et + OH⁻(H₂O)₁₆ was employed. For X = O, three elementary processes and for X = NH four ones were obtained. The rate-determining step of X = O is the first TS (TS1, the OH⁻ addition step), while that of X = NH is TS2. TS2 of X = NH leads to a novel Mulliken charge-transfer complex, Ph–(OH)(O=)C∙∙∙N(H₂)–Et. The superiority or inferiority between the direct nucleophilic process or the general base-catalyzed process for TS1 was examined with the model Ph–C(=O)–X–Et + OH⁻(H₂O)_n, n = 3, 5, 8, 12, 16, 24 and 32. The latter process was calculated to be more favorable regardless of the number (n, except n = 3) of water molecules. The counter ion Na⁺ works unfavorably on the ester hydrolysis, particularly on TS1. A minimal model of TS1 was proposed and was found to be insensitive to n.

Synthesis and evaluation of new guanidine-thiourea organocatalyst for the nitro-Michael reaction: Theoretical studies on mechanism and enantioselectivity

A new guanidine-thiourea organocatalyst has been developed and applied as bifunctional organocatalyst in the Michael addition reaction of diethyl malonate to trans-β-nitrostyrene. Extensive DFT calculations, including solvent effects and dispersion corrections, as well as ab initio calculations provide a plausible description of the reaction mechanism.

Relative Stabilities of Transition States Determine Diastereocontrol in Sulfur Ylide Additions onto Chiral N-Sulfinyl Imines

Additions of methylphenylsulfonium methylide onto chiral non-racemic N-sulfinyl imines (R'-SO-N=CH-R, R'=t-butyl, R=protected diol), followed by ring closure, yield terminal aziridines with high diastereoselectivity. Control reactions have established that both N- and C- iminyl substituents impact product preference, and when properly matched, one addition product is selected almost exclusively. Using solution-phase density functional computational methods, minima and transition state searches have been performed to reveal the structural origins of the diastereoselectivity. Our computational findings indicate that ring closure is fast and irreversible, and consequently, the relative energies of the transition states for the competing Re/Si addition steps determine the product diastereomeric ratios. Analysis of addition transition state structures reveals the causes of selectivity as arising from the N- and C- iminyl substituents, and we identify the S (R) configuration of the N-sulfinyl sulfur atom as the dominant director of Si (Re) addition. The control attributed to the sulfur configuration is tied to an important favorable internal interaction between the sulfinyl oxygen and the iminyl hydrogen. The protected diol acts as a secondary director, owing to steric/electrostatic interactions with the approaching ylide.

Transition states and origins of 1,4-asymmetric induction in alkylations of 2,2,6-trialkylpiperidine enamines

The asymmetric C-alkylation of chiral enamines derived from terminal epoxides and lithium 2,2,6-trialkylpiperidides has previously been shown to provide alpha-alkylated aldehydes by intermolecular nucleophilic substitution in good levels of asymmetric induction. We now report a computational study of the origins of asymmetric induction in these reactions. Computational modeling with density functional theory (B3LYP/6-31G(d)) agrees closely with the experimental observations. This stereoselectivity is attributed to a preferential conformation of the enamine and the piperidine ring that places the C-6 alkyl substituent in an axial position due to A(1, 3) strain. Preferential attack occurs away from the axial group, for steric reasons. The effects of changing the C-6 substituent from methyl to isopropyl were studied, and twist transition states were found to contribute significantly in the latter alkylations.

Applied implications of reinforcement history effects

Although the influence of reinforcement history is a theoretical focus of behavior analysis, the specific behavioral effects of reinforcement history have received relatively little attention in applied research and practice. We examined the potential effects of reinforcement history by reviewing nonhuman, human operant, and applied research and interpreted the findings in relation to possible applied significance. The focus is on reinforcement history effects in the context of reinforcement schedules commonly used either to strengthen behavior (e.g., interval schedules) or commonly used to decrease behavior (e.g., extinction).

The veils of clio: dimensions of a behavioral narratology

This paper outlines a behavior-analysis approach to the field of narratology, the study of the narrative or story, with emphasis on nonfiction stories and the processes by which such stories distort the world they describe. Stories are described in terms of (a) a behavior-analysis adaptation of Todorov's (1977) analysis of the plots of stories in terms of states of equilibrium/disequilibrium and (b) Grant's (2005) analysis of the structure of stories in terms of establishing operations and escape contingencies. These two sets of concepts are applied to understanding how and why stories lead to distortions of the events they report.

Despite slow catalysis and confused substrate specificity, all ribulose bisphosphate carboxylases may be nearly perfectly optimized

The cornerstone of autotrophy, the CO(2)-fixing enzyme, d-ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), is hamstrung by slow catalysis and confusion between CO(2) and O(2) as substrates, an "abominably perplexing" puzzle, in Darwin's parlance. Here we argue that these characteristics stem from difficulty in binding the featureless CO(2) molecule, which forces specificity for the gaseous substrate to be determined largely or completely in the transition state. We hypothesize that natural selection for greater CO(2)/O(2) specificity, in response to reducing atmospheric CO(2):O(2) ratios, has resulted in a transition state for CO(2) addition in which the CO(2) moiety closely resembles a carboxylate group. This maximizes the structural difference between the transition states for carboxylation and the competing oxygenation, allowing better differentiation between them. However, increasing structural similarity between the carboxylation transition state and its carboxyketone product exposes the carboxyketone to the strong binding required to stabilize the transition state and causes the carboxyketone intermediate to bind so tightly that its cleavage to products is slowed. We assert that all Rubiscos may be nearly perfectly adapted to the differing CO(2), O(2), and thermal conditions in their subcellular environments, optimizing this compromise between CO(2)/O(2) specificity and the maximum rate of catalytic turnover. Our hypothesis explains the feeble rate enhancement displayed by Rubisco in processing the exogenously supplied carboxyketone intermediate, compared with its nonenzymatic hydrolysis, and the positive correlation between CO(2)/O(2) specificity and (12)C/(13)C fractionation. It further predicts that, because a more product-like transition state is more ordered (decreased entropy), the effectiveness of this strategy will deteriorate with increasing temperature.