Reaction Coordinate Research Articles

C-H Bond Oxidation by MnIV-Oxo Complexes: Hydrogen-Atom Tunneling and Multistate Reactivity.

The reactivity of six MnIV-oxo complexes in C-H bond oxidation has been examined using a combination of kinetic experiments and computational methods. Variable-temperature studies of the oxidation of 9,10-dihydroanthracene (DHA) and ethylbenzene by these MnIV-oxo complexes yielded activation parameters suitable for evaluating electronic structure computations. Complementary kinetic experiments of the oxidation of deuterated DHA provided evidence for hydrogen-atom tunneling in C-H bond oxidation for all MnIV-oxo complexes. These results are in accordance with the Bell model, where tunneling occurs near the top of the transition-state barrier. Density functional theory (DFT) and DLPNO-CCSD(T1) computations were performed for three of the six MnIV-oxo complexes to probe a previously predicted multistate reactivity model. The DFT computations predicted a thermal crossing from the 4B1 ground state to a 4E state along the C-H bond oxidation reaction coordinate. DLPNO-CCSD(T1) calculations further confirm that the 4E transition state offers a lower energy barrier, reinforcing the multistate reactivity model for these complexes. We discuss how this multistate model can be reconciled with recent computations that revealed that the kinetics of C-H bond oxidation by this set of MnIV-oxo complexes can be well-predicted on the basis of the thermodynamic driving force for these reactions.

A review on dynamics of permeability-glycoprotein in efflux of chemotherapeutic drugs

Permeability-glycoprotein (P-gp) belongs to the ABS transporter protein family, with a high expression rate in cancerous cells. The substrate/inhibitors of the protein are structurally diverse, with no lucid mechanism of inhibition. There are two schools of thought on the inhibition mechanism: (i) P-gp inhibitors bind to the huge hydrophobic cavity between two Trans-Membrane Domains (TMDs), supported by ample literary proof and (ii) P-gp inhibitors bind to the vicinity of Nucleotide-Binding Sites (NBSs). Structural biologists have presented several experimental and theoretical structures of P-gp with bound nucleotides and inhibitors to explain the same. However, the available experimental P-gp structures are insufficient to address the catalytic transition path of mammalian P-gp in detail, thus the dynamics and mechanism by which drugs are effluxed is still unknown. Targeted Molecular Dynamics (targeted MD) could be used to minutely analyse and explore the catalytic transition inward open (IO) to outward open (OO) and relaxation path (OO to IO). Finally, analysis of targeted MD trajectory may help to explore different conformational states of Pg-p (reaction coordinate of catalytic transition/relaxation), efflux of compounds aided by the dynamics of Nucleotide Binding Domains/NBDs (ATP coupled process) and TMDs (peristalsis-like movement pushes the bound molecule). This review presents an understanding of the catalytic transition and dynamics of protein which provides insights at the efflux of chemotherapeutic drug using in cancer treatment.

Tandem hybridization chain reaction and selective coordination enable fluorescence detection of exosomes in lung cancer

Liquid biopsy based on tumor-derived exosomes (TDEs) is potentially effective in assisting early cancer diagnosis. However, accurate quantification of the approach remains challenging due to the low concentration and heterogeneity of TDEs. This work involved designing a homogeneous enzyme-free fluorescent sensing strategy by targeting programmed cell death ligand 1 (PD-L1) that was overexpressed on the surface of TDEs, coupled with the tandem hybridization chain reaction (HCR) and the selective coordination of Cu2+. The aptamer was used as a specific recognition probe for binding with the target protein, thereby regulating the tandem HCR reactions and achieving signal amplification. The coordination between Cu2+ and double-stranded DNA (dsDNA) can further regulate the fluorescence intensity of the signal molecule, calcein, for precise quantification of TDEs. The results showed that the detection limit (LOD) for TDEs can be as low as 100 particles/mL. Moreover, the proposed strategy can accurately differentiate between lung cancer patients (n = 25) and healthy donors (n = 12), with a sensitivity of 92%, specificity of 100%, and an area under the receiver operating characteristic curve (AUC) of 0.963. The fluorescence analysis also demonstrated a strong correlation with the computed tomography scans and pathological analysis. Therefore, the proposed method in this study can provide more insights into assisting in the early diagnosis of lung cancer through TDEs-based liquid biopsy.

Intermolecular interaction of azide, cyano and alkyne-N-phenethylacetamide dimers: Experimental and quantum chemical approach

In this study, we present the synthesis and structure characterization by single-crystal X-ray Diffraction (SC-XRD), Ultraviolet Spectroscopy (UV), Fourier Transform Infrared Spectroscopy (FTIR), Nuclear Magnetic Resonance (NMR) and High-resolution Mass Spectrometry (HRMS) of 2-azido-N-phenethylacetamide (4) and 2-cyano-N-phenethylacetamide (6). Further, Density Functional Theory (DFT) was employed to get a better insight regarding the properties exhibited by the compounds. The computational chemistry has been used to explain and investigate the bimolecular nucleophilic substitution (SN2) and concerted acyl substitution mechanisms for the synthesis of compounds 4 and 6, respectively. Additionally, intrinsic reaction coordinate (IRC) calculations confirm the transition state for these reactions. The X-ray diffraction analysis showed that the compounds 4 and 6 crystallized as monoclinic systems, in space group P21/c and P21/n, respectively. The Hirshfeld Surface Analysis revealed that the main contributions in the crystal packing have H···H, H···N/N···H, H···C/C···H and H···O/O···H interactions. The frontier molecular orbital energies were calculated and the HOMO-LUMO energy gap of 4 and 6 were 10.011 and 10.278 eV, respectively. Theoretical values of electronic transitions, vibrational frequencies and NMR chemical shifts were calculated and compared with experimental results, they all showed good results.

Derivation of the Invariant Free-Energy Landscape Based on Langevin Dynamics.

A conventionally defined free-energy landscape (FEL) exhibits unphysical dependence on the choice of reaction coordinates and hence lacks universal predictive ability. We here show that three physically plausible requirements uniquely determine the FEL formula for a given reaction coordinate. Our FEL is expressed solely in terms of quantities obtained through time-series data analysis, namely, the probability distribution and the diffusion matrix. It is free from any unphysical coordinate dependence and coincides with the conventional FEL in special cases. The uniqueness and robustness of the formula strongly suggest that our FEL has universal predictive power.

The reaction mechanism of the Ideonella sakaiensis PETase enzyme

Polyethylene terephthalate (PET), the most abundantly produced polyester plastic, can be depolymerized by the Ideonella sakaiensis PETase enzyme. Based on multiple PETase crystal structures, the reaction has been proposed to proceed via a two-step serine hydrolase mechanism mediated by a serine-histidine-aspartate catalytic triad. To elucidate the multi-step PETase catalytic mechanism, we use transition path sampling and likelihood maximization to identify optimal reaction coordinates for the PETase enzyme. We predict that deacylation is likely rate-limiting, and the reaction coordinates for both steps include elements describing nucleophilic attack, ester bond cleavage, and the “moving-histidine” mechanism. We find that the flexibility of Trp185 promotes the reaction, providing an explanation for decreased activity observed in mutations that restrict Trp185 motion. Overall, this study uses unbiased computational approaches to reveal the detailed reaction mechanism necessary for further engineering of an important class of enzymes for plastics bioconversion.

Role of the Vibrational and Translational Energies in the CN(v)+C2H6(ν1, ν2, ν5 and ν9) Reactions. A Theoretical QCT Study.

Quasi-classical trajectory (QCT) calculations were conducted on the newly developed full-dimensional potential energy surface, PES-2023, to analyse two critical aspects: the influence of vibrational versus translational energy in promoting reactivity, and the impact of vibrational excitation within similar vibrational modes. The former relates to Polanyi's rules, while the latter concerns mode selectivity. Initially, the investigation revealed that independent vibrational excitation by a single quantum of ethane's symmetric and asymmetric stretching modes (differing by only 15 cm-1) yielded comparable dynamics, reaction cross-sections, HCN(v) vibrational product distributions, and scattering distributions. This observation dismisses any significant mode selectivity. Moreover, an equivalent amount of energy provided as translational energy (at total energies of 9.6 and 20.0 kcal mol-1) gave rise to slightly lower reactivity compared to the same amount of energy provided as vibrational energy. This effect is more evident at low energies, presenting a counterintuitive scenario in an 'early transition state' reaction. These findings challenge the straightforward application of Polanyi's rules in polyatomic systems. Regarding CN(v) vibrational excitation, our calculations reveal that the reaction cross-section remains practically unaffected by this vibrational excitation, suggesting that the CN stretching mode is a spectator mode. The results were rationalized by considering several factors: the strong coupling between different vibrational modes, and between vibrational modes and the reaction coordinate; and a significant vibrational energy redistribution within the ethane reactant before collision. This redistribution creates an unphysical energy flow, resulting in loss of adiabaticity and vibrational memory before the reactants' collision. These theoretical findings require future confirmation through experimental or theoretical quantum mechanical studies, which are currently unavailable.

ELViM: Exploring Biomolecular Energy Landscapes through Multidimensional Visualization.

Molecular dynamics (MD) simulations provide a powerful means of exploring the dynamic behavior of biomolecular systems at the atomic level. However, analyzing the vast data sets generated by MD simulations poses significant challenges. This article discusses the energy landscape visualization method (ELViM), a multidimensional reduction technique inspired by the energy landscape theory. ELViM transcends one-dimensional representations, offering a comprehensive analysis of the effective conformational phase space without the need for predefined reaction coordinates. We apply the ELViM to study the folding landscape of the antimicrobial peptide Polybia-MP1, showcasing its versatility in capturing complex biomolecular dynamics. Using dissimilarity matrices and a force-scheme approach, the ELViM provides intuitive visualizations, revealing structural correlations and local conformational signatures. The method is demonstrated to be adaptable, robust, and applicable to various biomolecular systems.

Enhanced Sampling of Configuration and Path Space in a Generalized Ensemble by Shooting Point Exchange.

The computer simulation of many molecular processes is complicated by long timescales caused by rare transitions between long-lived states. Here, we propose a new approach to simulate such rare events, which combines transition path sampling with enhanced exploration of configuration space. The method relies on exchange moves between configuration and trajectory space, carried out based on a generalized ensemble. This scheme substantially enhances the efficiency of the transition path sampling simulations, particularly for systems with multiple transition channels, and yields information on thermodynamics, kinetics and reaction coordinates of molecular processes without distorting their dynamics. The method is illustrated using the isomerization of proline in the KPTP tetrapeptide.

Pseudo-marginal approximation to the free energy in a micro-macro Markov chain Monte Carlo method.

We introduce a generalized micro-macro Markov chain Monte Carlo (mM-MCMC) method with pseudo-marginal approximation to the free energy that is able to accelerate sampling of the microscopic Gibbs distributions when there is a time-scale separation between the macroscopic dynamics of a reaction coordinate and the remaining microscopic degrees of freedom. The mM-MCMC method attains this efficiency by iterating four steps: (i) propose a new value of the reaction coordinate, (ii) accept or reject the macroscopic sample, (iii) run a biased simulation that creates a microscopic molecular instance that lies close to the newly sampled macroscopic reaction coordinate value, and (iv) microscopic accept/reject step for the new microscopic sample. In the present paper, we eliminate the main computational bottleneck of earlier versions of this method: the necessity to have an accurate approximation of free energy. We show that the introduction of a pseudo-marginal approximation significantly reduces the computational cost of the microscopic accept/reject step while still providing unbiased samples. We illustrate the method's behavior on several molecular systems with low-dimensional reaction coordinates.

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.

Localized Plasmonic Heating for Single-Molecule DNA Rupture Measurements in Optical Tweezers.

To date, studies on the thermodynamic and kinetic processes that underlie biological function and nanomachine actuation in biological- and biology-inspired molecular constructs have primarily focused on photothermal heating of ensemble systems, highlighting the need for probes that are localized within the molecular construct and capable of resolving single-molecule response. Here we present an experimental demonstration of wavelength-selective, localized heating at the single-molecule level using the surface plasmon resonance of a 15 nm gold nanoparticle (AuNP). Our approach is compatible with force-spectroscopy measurements and can be applied to studies of the single-molecule thermodynamic properties of DNA origami nanomachines as well as biomolecular complexes. We further demonstrate wavelength selectivity and establish the temperature dependence of the reaction coordinate for base-pair disruption in the shear-rupture geometry, demonstrating the utility and flexibility of this approach for both fundamental studies of local (nanometer-scale) temperature gradients and rapid and multiplexed nanomachine actuation.

Thermal isomerization rates in retinal analogues using Ab-Initio molecular dynamics.

For a detailed understanding of chemical processes in nature and industry, we need accurate models of chemical reactions in complex environments. While Eyring transition state theory is commonly used for modeling chemical reactions, it is most accurate for small molecules in the gas phase. A wide range of alternative rate theories exist that can better capture reactions involving complex molecules and environmental effects. However, they require that the chemical reaction is sampled by molecular dynamics simulations. This is a formidable challenge since the accessible simulation timescales are many orders of magnitude smaller than typical timescales of chemical reactions. To overcome these limitations, rare event methods involving enhanced molecular dynamics sampling are employed. In this work, thermal isomerization of retinal is studied using tight-binding density functional theory. Results from transition state theory are compared to those obtained from enhanced sampling. Rates obtained from dynamical reweighting using infrequent metadynamics simulations were in close agreement with those from transition state theory. Meanwhile, rates obtained from application of Kramers' rate equation to a sampled free energy profile along a torsional dihedral reaction coordinate were found to be up to three orders of magnitude higher. This discrepancy raises concerns about applying rate methods to one-dimensional reaction coordinates in chemical reactions.

Formic Acid-Ammonia Heterodimer: A New Δ-Machine Learning CCSD(T)-Level Potential Energy Surface Allows Investigation of the Double Proton Transfer.

The formic acid-ammonia dimer is an important example of a hydrogen-bonded complex in which a double proton transfer can occur. Its microwave spectrum has recently been reported and rotational constants and quadrupole coupling constants were determined. Calculated estimates of the double-well barrier and the internal barriers to rotation were also reported. Here, we report a full-dimensional potential energy surface (PES) for this complex, using two closely related Δ-machine learning methods to bring it to the CCSD(T) level of accuracy. The PES dissociates smoothly and accurately. Using a 2d quantum model the ground vibrational-state tunneling splitting is estimated to be less than 10-4 cm-1. The dipole moment along the intrinsic reaction coordinate is calculated along with a Mullikan charge analysis and supports the mildly ionic character of the minimum and strongly ionic character at the double-well barrier.

Optimal control of N-H photodissociation of pyridinyl.

The N-H photodissociation dynamics of the pyridinyl radical upon continuous excitation to the optically bright, first excited ππ* electronic state by an ultra-violet (UV) laser pulse has been investigated within the mathematical framework of optimal control theory. The genetic algorithm (GA) is employed as the optimization protocol. We considered a three-state and three-mode model Hamiltonian, which includes the reaction coordinate, R (a1 symmetry); the coupling coordinates (namely, out-of-plane bending coordinate of the hydrogen atom of azine group), Θ (b1 symmetry); and the wagging mode, Q9 (a2 symmetry). The three electronic states are the ground, ππ*, and πσ* states. The πσ* state crosses both the ground state and the ππ* state, and it is a repulsive state on which N-H dissociation occurs upon photoexcitation. Different vibrational wave functions along the coupling coordinates, Θ and Q9, of the ground electronic state are used as the initial condition for solving the time-dependent Schrödinger equation. The optimal UV laser pulse is designed by applying the GA, which maximizes the dissociation yield. We obtained over 95% dissociation yield through the πσ* asymptote using the optimal pulse of a time duration of ∼30 000a.u. (∼725.66fs).

Synthesis, Characterization, Crystal Structure, and Theoretical Calculations of Novel 1,5-Benzodiazepine Derivatives Obtained via 1,3-Dipolar Cycloaddition Reactions

A series of triazolo-benzodiazepine derivatives were synthesized by the condensation of 2,2,4-trimethyl-2,3-dihydro-1H-1,5-benzodiazepine (BZD) 1 with nitrilimine analogs (N-aryl-C-ethoxycarbonyl-nitrilimines and diarylnitrilimines). The newly synthesized cycloadducts were well-characterized by various spectroscopic techniques (1H, 13C NMR, and HRMS). The structure of single-crystal was characterized using a single-crystal X-ray technique. A theoretical study of the chemo and regioselectivity has been performed by density functional theory at the B3LYP/6-311G(d,p) level of theory. A comprehensive theoretical study of the reaction mechanism was performed. The geometry of the different reactants and products were analyzed, the transition states were located and the corresponding reaction paths were determined and characterized by the intrinsic reaction coordinate. Computational results show that the reactions were completely chemo and regioselective, the mechanism of reactions was non-concerted and explained the effect of aryl groups on the reaction yield.

Surface-Accelerated String Method for Locating Minimum Free Energy Paths.

We present a surface-accelerated string method (SASM) to efficiently optimize low-dimensional reaction pathways from the sampling performed with expensive quantum mechanical/molecular mechanical (QM/MM) Hamiltonians. The SASM accelerates the convergence of the path using the aggregate sampling obtained from the current and previous string iterations, whereas approaches like the string method in collective variables (SMCV) or the modified string method in collective variables (MSMCV) update the path only from the sampling obtained from the current iteration. Furthermore, the SASM decouples the number of images used to perform sampling from the number of synthetic images used to represent the path. The path is optimized on the current best estimate of the free energy surface obtained from all available sampling, and the proposed set of new simulations is not restricted to being located along the optimized path. Instead, the umbrella potential placement is chosen to extend the range of the free energy surface and improve the quality of the free energy estimates near the path. In this manner, the SASM is shown to improve the exploration for a minimum free energy pathway in regions where the free energy surface is relatively flat. Furthermore, it improves the quality of the free energy profile when the string is discretized with too few images. We compare the SASM, SMCV, and MSMCV using 3 QM/MM applications: a ribozyme methyltransferase reaction using 2 reaction coordinates, the 2'-O-transphosphorylation reaction of Hammerhead ribozyme using 3 reaction coordinates, and a tautomeric reaction in B-DNA using 5 reaction coordinates. We show that SASM converges the paths using roughly 3 times less sampling than the SMCV and MSMCV methods. All three algorithms have been implemented in the FE-ToolKit package made freely available.

In silico drug derivatives for KRAS-G12D: free-energy surfaces in aqueous solution by well-tempered metadynamics simulations

KRAS oncogenes are the largest family of mutated RAS isoforms, participating in about 30% of all cancers. Due to their paramount medical importance, enormous effort is being devoted to the development of inhibitors using clinical tests, wet-lab experiments and drug design, being this a preliminary step in the process of creating new drugs, prior to synthesis and clinical testing. One central aspect in the development of new drugs is the characterisation of all species that can be used for treatment. In this aim, we propose a computational framework based on combined all-atom molecular dynamics and metadynamics simulations in order to accurately access the most stable conformational variants for several derivatives of a recently proposed small-molecule, called DBD15-21-22. Free energy calculations are essential to unveil mechanisms at the atomic scale like binding affinities or dynamics of stable states. Considering specific atom-atom distances and torsional angles as reliable reaction coordinates we have obtained free-energy landscapes by well-tempered metadynamics simulations, revealing local and global minima of the free-energy hypersurface. We have observed that a variety of stable states together with transition states are clearly detected depending on the particular species, leading to predictions on the behaviour of such compounds in ionic aqueous solution.

Capture of CO2 by Melamine Derivatives: A DFT Study Combining the Relative Energy Gradient Method with an Interaction Energy Partitioning Scheme.

A theoretical study of the interaction between melamine and CO2 was carried out using density functional theory (DFT) with the B3LYP-D3(BJ)/aug-cc-pVTZ level of theory. The presence of anions interacting with melamine transforms the weakly bonded tetrel complexes into adducts. Thus, melamine acts as an FLP (frustrated Lewis pair) with acid groups (NHs as hydrogen bond donors) and a base group (N of the triazine ring). The application of the relative energy gradient formalism (REG) along the reaction coordinate has demonstrated that the ability of the melamine-anion systems to capture CO2 is linked to its capacity to polarize the CO2 molecule. These results have been confirmed by placing the melamine:CO2 complex in a uniform electric field with different strengths.

Snapshots of the Reaction Coordinate of a Thermophilic 2'-Deoxyribonucleoside/ribonucleoside Transferase.

Nucleosides are ubiquitous to life and are required for the synthesis of DNA, RNA, and other molecules crucial for cell survival. Despite the notoriously difficult organic synthesis of nucleosides, 2'-deoxynucleoside analogues can interfere with natural DNA replication and repair and are successfully employed as anticancer, antiviral, and antimicrobial compounds. Nucleoside 2'-deoxyribosyltransferase (dNDT) enzymes catalyze transglycosylation via a covalent 2'-deoxyribosylated enzyme intermediate with retention of configuration, having applications in the biocatalytic synthesis of 2'-deoxynucleoside analogues in a single step. Here, we characterize the structure and function of a thermophilic dNDT, the protein from Chroococcidiopsis thermalis (CtNDT). We combined enzyme kinetics with structural and biophysical studies to dissect mechanistic features in the reaction coordinate, leading to product formation. Bell-shaped pH-rate profiles demonstrate activity in a broad pH range of 5.5-9.5, with two very distinct pKa values. A pronounced viscosity effect on the turnover rate indicates a diffusional step, likely product (nucleobase1) release, to be rate-limiting. Temperature studies revealed an extremely curved profile, suggesting a large negative activation heat capacity. We trapped a 2'-fluoro-2'-deoxyarabinosyl-enzyme intermediate by mass spectrometry and determined high-resolution structures of the protein in its unliganded, substrate-bound, ribosylated, 2'-difluoro-2'-deoxyribosylated, and in complex with probable transition-state analogues. We reveal key features underlying (2'-deoxy)ribonucleoside selection, as CtNDT can also use ribonucleosides as substrates, albeit with a lower efficiency. Ribonucleosides are the building blocks of RNA and other key intracellular metabolites participating in energy and metabolism, expanding the scope of use of CtNDT in biocatalysis.