Transition State Of Reaction Research Articles

Glycerol 3-Phosphate Dehydrogenase: Role of the Protein Conformational Change in Activation of a Readily Reversible Enzyme-Catalyzed Hydride Transfer Reaction.

Kinetic parameters are reported for glycerol 3-phosphate dehydrogenase (GPDH)-catalyzed hydride transfer from the whole substrate glycerol 3-phosphate (G3P) or truncated substrate ethylene glycol (EtG) to NAD, and for activation of the hydride transfer reaction of EtG by phosphite dianion. These kinetic parameters were combined with parameters for enzyme-catalyzed hydride transfer in the microscopic reverse direction to give the reaction equilibrium constants Keq. Hydride transfer from G3P is favored in comparison to EtG because the carbonyl product of the former reaction is stabilized by hyperconjugative electron donation from the -CH2R keto substituent. The kinetic data show that the phosphite dianion provides the same 7.6 ± 0.1 kcal/mol stabilization of the transition states for enzyme-catalyzed reactions in the forward [reduction of NAD by EtG] and reverse [oxidation of NADH by glycolaldehyde] directions. The experimental evidence that supports a role for phosphite dianion in stabilizing the active closed form of the GPDH (EC) relative to the ca. 6 kcal/mol more unstable open form (EO) is summarized.

Investigation on Catalytic Cracking Performance of Metal Catalysts for 1,1,2‐TCE

AbstractPVDC played an irreplaceable role in the field of sealed packaging, and its polymer monomer, VDC, was in short supply. At present, the saponification of 1,1,2‐TCE and sodium hydroxide was used to generate VDC in industry, which was a process with great environmental pollution. Catalytic dehydrochlorination of 1,1,2‐TCE to produce VDC was a green process route, but the selection of catalysts had always been controversial. This study aimed to screen catalysts suitable for industrial applications. The cesium based catalysts with good catalytic performance were systematically characterized and evaluated, and the overall reaction process was calculated using DFT calculation. The experimental results indicated that the cesium chloride catalyst with a 3 % molar fraction had the best catalytic performance, achieving 55.27 % conversion of 1,1,2‐TCE and 76.85 % selectivity for VDC, respectively. The reaction paths and transition state of several catalysts were calculated by DFT method. It was revealed that the activation energy required for the reaction of CsCl catalyst was the lowest, at 130.61 kcal/mol, and the energy of the product VDC was the lowest, at −63.25 kcal/mol, making it the most stable. The calculation results were consistent with the experimental data, indicating that cesium chloride catalyst had the best reaction performance. Therefore, the subsequent research could focus on the method of improving the supported dispersity of cesium chloride catalyst and the development of core‐shell catalyst to lay the foundation for further industrialization.

Recent Advances in π-Stacking Interaction-Controlled Asymmetric Synthesis.

The π-stacking interaction is one of the most important intramolecular and intermolecular noncovalent interactions in organic chemistry. It plays an important role in stabilizing some structures and transition states in certain reactions via both intramolecular and intermolecular interactions, facilitating different selectivities, such as chemo-, regio-, and stereoselectivities. This minireview focuses on the recent examples of the π-stacking interaction-controlled asymmetric synthesis, including auxiliary-induced asymmetric synthesis, kinetic resolution, asymmetric synthesis of helicenes and heterohelicenes, and multilayer 3D chiral molecules.

A Computational Perspective on the Reactivity of π-spacers in Self-Immolative Elimination Reactions.

The controlled release of chemicals, especially in drug delivery, is crucial, often employing "self-immolative" spacers to enhance reliability. These spacers separate the payload from the protecting group, ensuring a more controlled release. Over the years, design rules have been proposed to improve the elimination process's reaction rate by modifying spacers with electron-donating groups or reducing their aromaticity. The spacer design is critical for determining the range of functional groups released during this process. This study explores various strategies from the literature aimed at improving release rates, focusing on the electronic nature of the spacer, its aromaticity, the electronic nature of its substituents, and the leaving groups involved in the elimination reaction. Through computational analysis, I investigate activation free energies by identifying transition states for model reactions. My calculations align qualitatively with experimental results, demonstrating the feasibility and reliability of computationally pre-screening model self-immolative eliminations. This approach allows proposing optimal combinations of spacer and leaving group for achieving the highest possible release rate.

The formation of nickelalactone in CO2/C2H4 coupling reaction: A benchmark, dispersion correction, and energy decomposition analysis

The oxidative coupling of CO2 and ethylene for synthesizing acrylic acid and its derivatives is considered one of the “dream reactions” in catalysis. The formation of acrylic acid by CO2/C2H4 coupling is hardly possible due to the endothermic nature of the reaction. This work reports a comprehensive study of the nickelalactone formation from CO2/C2H4 coupling over Ni-catalysts. We have evaluated the accuracy of the DLPNO-CCSD(T) method in determining the barrier heights and the reaction energetics for the nickelalactone formation. Extrapolation to the complete basis set limit was performed using two-point extrapolation methods. It was found that the DLPNO-CCSD(T) method, in combination with the complete basis set cc-pVTZ/cc-pVQZ extrapolation, gives the error within 1.0 kcal/mol. To gain a molecular understanding of the formation of acrylic acid by CO2/C2H4 coupling, the distortion-interaction model was used as an energy decomposition method to analyze the inner- and outer-sphere reaction transition states, considering two competing pathways. It was found that i) the inner-sphere reaction is superior to the outer-sphere reaction owing to the lower distortion energy and stronger interactions, ii) three prominent pairs of orbital interactions exist between the Ni-C2H4 complex and the CO2 molecule, and iii) the dispersion correction is crucial to obtaining reliable non-covalent interaction energies.

Initial Decomposition Mechanism of NH3OH+N5- Crystal under Thermal and Shock Loading: A First-Principles Study.

NH3OH+N5- is a novel energetic material (EM) which has attracted much interest for its promising performances, including high energy density, high density, low sensitivity, and low toxicity. In this study, the initial decomposition mechanism of NH3OH+N5- crystal was investigated under thermal and shock loading by molecular dynamics simulation. First, programmed heating and constant temperature simulations were carried out by molecular dynamics simulation on the basis of density functional theory (DFT-MD). Results indicated that the initial decomposition reactions of NH3OH+N5- could be described by three reactions: proton transfer, ring-opening reaction, and cation decomposition and recombination, and three pathways of ring-opening reaction were found, including the ring-opening of N5-, HN5, and H2N6. The first two reactions are the main pathways that produce N2 molecules. Furthermore, we carried out DFT-MD simulations to study the shock decomposition behaviors of NH3OH+N5-, and three initial steps were proposed: N5-, HN5, and N6 ring-opening. The fewer N5- and HN5 ring-opening reactions were found during the shock simulation, accompanied by a significant change in the N5- bond angle. What's more, the transition states of decomposition reactions were investigated through quantum chemical calculations. The results revealed that the proton transfer reaction exhibits lower activation barriers compared to ring-opening reactions, and proton transfer would accelerate ring-opening reactions. In addition, the ring-opening reaction is the main energy-releasing reaction in the early stages of the decomposition. This work could promote the comprehension of the decomposition mechanism and energy release regularity of N5- ions.

Effect of ligand structure and metal center on ethylene oligomerization with N, N′ Schiff base late transition complexes: experiments and calculations

A series of N, N’ bis(pyridine-imine) Schiff base late transition metal (Fe, Co, and Ni) complexes with different ligand structures and catalytic active sites were synthesized. Ethylene oligomerization results showed that bis(pyridine-imine) iron complex had the highest catalytic activity (10.8 × 105 g/mol Fe h), and the catalytic activity of cobalt complex was the lowest (2.5 × 105 g/mol Co h); nickel complex had the highest selectivity toward high carbon olefins (28.6%), while the iron complex had the lowest (0.2%). The structure-activity relationship between the catalyst structure and catalytic properties for ethylene oligomerization was further studied by density functional theory (DFT) calculations. The bis(pyridine-imine) iron complex had the highest energy gap value and the most stable catalyst structure, which was more conducive to oligomerization; and the N–M–N bond of the nickel complex had the smallest bond angle, which was beneficial for chain growth. Based on the Cossee mechanism, a mechanism for ethylene oligomerization catalyzed by bis(pyridine-imine) metal complexes was proposed. To further study the micro reaction process of ethylene oligomerization, a molecular model of pyridine imine nickel complex and its catalytic ethylene oligomerization reaction path were proposed. The structure and energy of the reaction intermediate and transition state were calculated using DFT. The molecular model of the nickel complex had a lower ethylene insertion barrier and β-H elimination of energy barriers, indicating that the molecular model of the pyridine imine nickel complex had ethylene oligomerization active centers.

Metal-Free Activation of Molecular Oxygen by Quaternary Ammonium-Based Ionic Liquid: A Detail Mechanistic Study.

Most oxidation processes in common organic synthesis and chemical biology require transition metal catalysts or metalloenzymes. Herein, we report a detailed mechanistic study of a metal-free oxygen (O2) activation protocol on benzylamine/alcohols using simple quaternary alkylammonium-based ionic liquids to produce products such as amide, aldehyde, imine, and in some cases, even aromatized products. NMR and various control experiments established the product formation and reaction mechanism, which involved the conversion of molecular oxygen into a hydroperoxyl radical via a proton-coupled electron transfer process. Detection of hydrogen peroxide in the reaction medium using colorimetric analysis supported the proposed mechanism of oxygen activation. Furthermore, first-principles calculations using density functional theory (DFT) revealed that reaction coordinates and transition state spin densities have a unique spin conversion of triplet oxygen leading to formation of singlet products via a minimum energy crossing point. In addition to DFT, domain-based local pair natural orbital coupled cluster, (DLPNO-CCSD(T)), and complete active space self-consistent field, CASSCF(20,14) methods complemented the above findings. Partial density of states analysis showed stabilization of π* orbital of oxygen in the presence of ionic liquid, making it susceptible to hydrogen abstraction in a mild, metal-free condition. Inductively coupled plasma atomic emission spectroscopic (ICP-AES) analysis of reactant and ionic liquids clearly showed the absence of any significant transition metal contamination. The current results described the origin of O2 activation within the context of molecular orbital (MO) theory and opened up a new avenue for the use of ionic liquids as inexpensive, multifunctional and high-performance alternative to metal-based catalysts for O2 activation.

Changes in Mechanism and Transition State Structure for Solvolysis Reactions of Ring Substituted Benzyl Chlorides in Aqueous Solution.

Rate and product data are reported for the solvolysis reactions of twenty-seven mono, di (3,4) and tri (3,4,5) ring-substituted benzyl chlorides. The first order rate constant for solvolysis in 20% acetonitrile in water decrease from k solv = 2.2 s-1 for 4-methoxybenzyl chloride to 1.1 x 10-8 s-1 for 3,4-dinitrobenzyl chloride. The product rate constant ratios k MeOH/k TFE for solvolysis in 70/27/3 (v/v/v) HOH/TFE/MeOH range from a minimum of k MeOH/k TFE = 8 to a maximum of 110. The rate data were fit to a four-parameter Hammett equation that separates the resonance and polar effects of the aromatic ring substituents on the reaction rate. Increases in the values of the Hammett reaction constants and are observed as the substituent constants or are increased. A sharp decrease in the product selectivity k MeOH/k TFE = 26 for stepwise solvolysis of 4-methoxybenzyl chloride is observed as electron-withdrawing meta-substituents are added to 4-methoxybenzyl ring due to a Hammond-effect on the position of the transition state for solvent addition to the substituted 4-methoxybenzyl carbocation reaction intermediates. Sharp increases in the selectivity k MeOH/k TFE are observed with decreasing reactivity of other 3,4,5-subsituted benzyl chlorides due to anti-Hammond shifts on a two-dimensional More-O'Ferrall reaction coordinate diagram in the position of the transition state for a concerted solvolysis reaction.

Isofagomine Inhibits Multiple TcdB Variants and Protects Mice from Clostridioides difficile-Induced Mortality.

Clostridioides difficile causes life-threatening diarrhea and is one of the leading causes of nosocomial infections. During infection, C. difficile releases two gut-damaging toxins, TcdA and TcdB, which are the primary determinants of disease pathogenesis and are important therapeutic targets. Once in the cytosol of mammalian cells, TcdA and TcdB use UDP-glucose to glucosylate host Rho GTPases, which leads to cytoskeletal changes that result in a loss of intestinal integrity. Isofagomine inhibits TcdA and TcdB as a mimic of the glucocation transition state of the glucosyltransferase reaction. However, sequence variants of TcdA and TcdB across the clades of infective C. difficile continue to be identified, and therefore, evaluation of isofagomine inhibition against multiple toxin variants is required. Here, we show that isofagomine inhibits the glucosyltransferase domain of multiple TcdB variants and protects TcdB-induced cell rounding of the most common full-length toxin variants. Furthermore, we demonstrate that isofagomine protects against C. difficile-induced mortality in two murine models of C. difficile infection. Isofagomine treatment of mouse C. difficile infection also permitted the recovery of the gastrointestinal microbiota, an important barrier to preventing recurring C. difficile infection. The broad specificity of isofagomine supports its potential as a prophylactic to protect against C. difficile-induced morbidity and mortality.

Predicting Mutational Effects on Ca2+-Activated Chloride Conduction of TMEM16A Based on a Simulation Study.

The dysfunction and defects of ion channels are associated with many human diseases, especially for loss-of-function mutations in ion channels such as cystic fibrosis transmembrane conductance regulator mutations in cystic fibrosis. Understanding ion channels is of great current importance for both medical and fundamental purposes. Such an understanding should include the ability to predict mutational effects and describe functional and mechanistic effects. In this work, we introduce an approach to predict mutational effects based on kinetic information (including reaction barriers and transition state locations) obtained by studying the working mechanism of target proteins. Specifically, we take the Ca2+-activated chloride channel TMEM16A as an example and utilize the computational biology model to predict the mutational effects of key residues. Encouragingly, we verified our predictions through electrophysiological experiments, demonstrating a 94% prediction accuracy regarding mutational directions. The mutational strength assessed by Pearson's correlation coefficient is -0.80 between our calculations and the experimental results. These findings suggest that the proposed methodology is reliable and can provide valuable guidance for revealing functional mechanisms and identifying key residues of the TMEM16A channel. The proposed approach can be extended to a broad scope of biophysical systems.

Experimental and computational study of the thermal degradation of primary amines used in CO2 capture

CO2 loaded amine polymerizes during solvent regeneration at temperatures above 100 °C, resulting in the deterioration of solvent performance. Herein, five primary amines were heated to 120, 135 and 150 °C with CO2 loading of 0.4C/N to study thermal degradation. It was found that 2-amine-1-butanol showed the greatest amine loss of 38.5 % after heating to 135 °C for 672 hrs while 2-amino-2-methyl-1-propanol was most stable with amine loss of 17.4 % under the same conditions. The degradation products were identified and the reaction pathway was studied through density functional theory (DFT) calculation. Furthermore, the transition state for ring closure and opening reactions was analyzed. The ring closure reaction to form oxazolidinones had a higher energy barrier, showing that it was the limiting step. This is further supported by the good agreement with experimental results. The structure–activity relationship showed the strong steric hindrance effect and the methyl group at β-carbon improved the amine stability.

Investing in entropy: the strategy of cucurbit[n]urils to accelerate the intramolecular Diels-Alder cycloaddition reaction of tertiary furfuryl amines.

Cucurbit[n]urils, renowned for their host-guest chemistry, are becoming versatile biomimetic receptors. Herein, we report that cucurbit[7]uril (CB[7]) accelerates the intramolecular Diels-Alder (IMDA) reaction for previously elusive and unreactive tertiary N-methyl-N-(homo)allyl-2-furfurylamines by up to 4 orders of magnitude under mild conditions. Using 1H NMR titrations and ITC experiments, we characterize the dissimilar thermodynamic and kinetic properties of the complexes. We also determine the activation parameters (ΔG ≠, ΔH ≠ and ΔS ≠) leading to the transition state of the IMDA reactions, both in the bulk and included in CB[7], to shed light on the key role of the receptor on the acceleration observed. CB[7] acts as an "entropy trap" utilizing guest binding to primarily pay the entropy penalty for reorganizing the substrate in a high-energy reactive conformation that resembles the geometry of the highly ordered transition state required for the IMDA reaction. This study underscores the potential of cucurbit[n]urils as artificial active sites, emulating specific aspects of enzymatic catalysis.

Quantum dynamics study of C—H stretching vibrational excitation in the F+CHD<sub>3</sub> → HF+CD<sub>3</sub> reaction

In recent decades, significant progress has been made in the precise theoretical investigation of gas-phase chemical reactions. Presently, a major challenge in the field of quantum dynamics is to develop the precise methodologies for studying chemical reactions involving more than four atoms. As a typical multi-atomic reaction system, the F+CH<sub>4</sub> reaction and its isotopic substitution reactions have attracted widespread attention from both experimental and theoretical perspectives in recent years. Experimental studies on the reaction of F+CHD<sub>3</sub> have revealed that the stretching vibration excitation of the C—H bond inhibits the bond dissociation, favoring the formation of DF+CHD<sub>2</sub> product channels. In this study, we use a seven-dimensional quantum time-dependent wave packet method to investigate the dynamics of the F+CHD<sub>3</sub> reaction in both the reactant vibrational ground state and the first stretching excited state of the C—H bond. In this work, the reaction probabilities under different vibrational conditions are analyzed, showing that when the collision energy is below 0.06 eV, the reaction probability curves exhibit numerous fast-oscillating peaks, supporting the experimentally suggested phenomena of dynamic resonance. In a collision energy range from 0.06 eV to 0.3 eV, the reaction probability for the HF product channel in the vibrational excited state is lower than that in the ground state, which is consistent with experimental observation. Through the analysis of the time-independent wave functions of product channels under low-energy collision conditions, it is found that for reactions involving vibrational ground states, the HF products in the product asymptotic region and the reaction transition state region are in the <i>v'</i> = 2 excited state and <i>v'</i> = 3 excited state of stretching vibration, respectively, which are consistent with previous experimental observations and six-dimensional quantum wave packet simulations. For reactions involving the first excited state of C—H stretching vibration, the HF products in the product asymptotic region and the reaction transition state region are both in the <i>v'</i> = 3 excited state of stretching vibration, which are consistent with the results obtained based on energy analysis. Simulation results indicate that in the case of low-energy collisions, the time-independent wave function for the C—H stretching vibrational excited state tends to be closer to the D atom side in the transition state region. This phenomenon is attributed to the more significant energy advantage of the vibrational excited state potential energy surface in the large collision angle region, explaining the inhibitory effect of stretching vibration excitation on the HF product channel. This study offers important theoretical support for explaining experimental results and contributes to a more in-depth understanding of the influence of vibrational mode excitations on the dynamical processes in poly-atomic reactions.

Structural analysis and molecular substrate recognition properties of Arabidopsis thaliana ornithine transcarbamylase, the molecular target of phaseolotoxin produced by Pseudomonas syringae.

Halo blight is a plant disease that leads to a significant decrease in the yield of common bean crops and kiwi fruits. The infection is caused by Pseudomonas syringae pathovars that produce phaseolotoxin, an antimetabolite which targets arginine metabolism, particularly by inhibition of ornithine transcarbamylase (OTC). OTC is responsible for production of citrulline from ornithine and carbamoyl phosphate. Here we present the first crystal structures of the plant OTC from Arabidopsis thaliana (AtOTC). Structural analysis of AtOTC complexed with ornithine and carbamoyl phosphate reveals that OTC undergoes a significant structural transition when ornithine enters the active site, from the opened to the closed state. In this study we discuss the mode of OTC inhibition by phaseolotoxin, which seems to be able to act only on the fully opened active site. Once the toxin is proteolytically cleaved, it mimics the reaction transition state analogue to fit inside the fully closed active site of OTC. Additionally, we indicate the differences around the gate loop region which rationally explain the resistance of some bacterial OTCs to phaseolotoxin.

Intermolecular interactions and the weakly bound precursor states of elementary physicochemical processes

This study concerns the importance of the precursor (or pre-reactive) state of elementary physicochemical processes whose basic features, as structure, stability, and trapping effect of reagents, are controlled by the balance of intermolecular forces that arise at long range and operate at intermediate and short separation distances. The detailed formulation of such forces, determining formation probability and dynamical evolution of the precursor state, is of relevance in molecular science and difficult to be treated by quantum chemistry. Such a problem has been tackled by us exploiting the phenomenological approach, which employs semi-empirical and empirical formulas to represent strength, range and angular dependence of the leading interaction components involved. In addition to the study of transport phenomena, part of the attention is addressed to chemi-ionization (or Penning ionization) reactions for which neutral reagents lead to atomic and/or molecular ions plus electrons as products. Chemi-ionizations are bimolecular processes occurring in several environments of interest, where a reagent is a species, formed in excited-metastable electronic states by collisions with energetic electrons or cosmic rays. For such reactions all crucial electronic rearrangements, affecting stability and evolution of the weakly bound precursor state, here coincident with the reaction transition state, are characterized with a high detail. The results of the present study are of interest for many other processes, whose precursor states and their relevant features are difficult to characterize, often masked by several other effects.Graphical abstract

Boosting quantum amplitude exponentially in variational quantum algorithms

We introduce a family of variational quantum algorithms, which we coin as quantum iterative power algorithms (QIPAs), and demonstrate their capabilities as applied to global-optimization numerical experiments. Specifically, we demonstrate the QIPA based on a double exponential oracle as applied to ground state optimization of the H 2 molecule, search for the transmon qubit ground-state, and biprime factorization. Our results indicate that QIPA outperforms quantum imaginary time evolution (QITE) and requires a polynomial number of queries to reach convergence even with exponentially small overlap between an initial quantum state and the final desired quantum state, under some circumstances. We analytically show that there exists an exponential amplitude amplification at every step of the variational quantum algorithm, provided the initial wavefunction has non-vanishing probability with the desired state and that the unique maximum of the oracle is given by , while all other values are given by the same value (here λ can be taken as eigenvalues of the problem Hamiltonian). The generality of the global-optimization method presented here invites further application to other problems that currently have not been explored with QITE-based near-term quantum computing algorithms. Such approaches could facilitate identification of reaction pathways and transition states in chemical physics, as well as optimization in a broad range of machine learning applications. The method also provides a general framework for adaptation of a class of classical optimization algorithms to quantum computers to further broaden the range of algorithms amenable to implementation on current noisy intermediate-scale quantum computers.

Investigating of transition state on the Pd–Au decorated ZnO nanoparticle layers for gas sensor application

In this work, the mechanism of the transition state of electron transfer reaction on the surface of the ZnO nanoparticles-based gas sensor has been investigated. The deposited ZnO nanoparticles thick films on glass slides had been synthesized by the current heating method and modified its surface by coating novel metals of gold and palladium with a sputtering technique with different sputtering times of 45–180 s. Field emission electron microscopy (FE-SEM), x-ray diffraction spectroscopy (XRD), and energy dispersive spectroscopy (EDS) were used for the characterization of ZnO nanoparticle thick films. After that, the reflectance spectra of films were investigated using Near-IR spectroscopy in the range of 900–2500 nm to study the surface absorption efficiency. The decrease in reflectance spectra was observed for conditions over 90 s of sputtering time. The particle size distribution and zeta potential of ZnO nanoparticles were analyzed using the dynamic light scattering technique for the calculation of particle size and the electrical charge potential. The results showed that the size particle distribution ranged from 155 to 245 nm and the more extensive range of 360–1100 nm. The optimized zeta potential of −14.44 mV was exhibited at the sputtering time of 45 s. Finally, the gas sensing mechanism in terms of surface charge density was proposed and used to explain the sensitivity enhancement of both resistive and capacitive gas sensors.

Reactivity of Group 5 and 6 Single-Site Photocatalysts for Partial Oxidation of Methane: Comparison of Chromium, Niobium, and Tungsten-Doped Mesoporous Amorphous Silica.

Single-site transition-metal-doped photocatalysts can potentially be used for partial oxidation of methane (POM) at remote sites where natural gas is extracted and methane is often flared or released to the atmosphere. While there have been several investigations into the performance of vanadium, there has been no general survey of the performance of other metals. This work aims and examines Cr, Nb, and W metal oxide materials embedded in amorphous SiO2 to determine the viability of each metal in catalyzing the POM. Photoexcited states are examined to determine the nature of the photoactivated species, and then the subsequent POM reaction mechanisms are elucidated. Using the calculated energies of reaction intermediates and transition states, the rate of methanol formation is evaluated through the use of a microkinetic model. The findings indicate that all three metals are potentially more suitable for catalyzing POM than vanadium but that niobium shows the most favorable energy profile.

CRISPR-Cas9 Activities with Truncated 16-Nucleotide RNA Guides Are Tuned by Target Duplex Stability Beyond the RNA/DNA Hybrid.

CRISPR-Cas9 has been adapted as a readily programmable genome manipulation agent, and continuing technological advances rely on an in-depth mechanistic understanding of Cas9 target discrimination. Cas9 interrogates a target by unwinding the DNA duplex to form an R-loop, where the RNA guide hybridizes with one of the DNA strands. It has been shown that RNA guides shorter than the normal length of 20-nucleotide (-nt) support Cas9 cleavage activity by enabling partial unwinding beyond the RNA/DNA hybrid. To investigate whether DNA segment beyond the RNA/DNA hybrid can impact Cas9 target discrimination with truncated guides, Cas9 double-stranded DNA cleavage rates (kcat) were measured with 16-nt guides on targets with varying sequences at +17 to +20 positions distal to the protospacer-adjacent-motif (PAM). The data reveal a log-linear inverse correlation between kcat and the PAM+(17-20) DNA duplex dissociation free energy (ΔGNN(17-20)0), with sequences having smaller ΔGNN(17-20)0 showing faster cleavage and a higher degree of unwinding. The results indicate that, with a 16-nt guide, "peripheral" DNA sequences beyond the RNA/DNA hybrid contribute to target discrimination by tuning the cleavage reaction transition state through the modulation of PAM-distal unwinding. The finding provides mechanistic insights for the further development of strategies that use RNA guide truncation to enhance Cas9 specificity.