Other affiliations: Texas Tech University
Bio: Manikandan Paranjothy is an academic researcher from Indian Institute of Technology, Jodhpur. The author has contributed to research in topic(s): Dissociation (chemistry) & Molecule. The author has an hindex of 7, co-authored 20 publication(s) receiving 172 citation(s). Previous affiliations of Manikandan Paranjothy include Texas Tech University.
TL;DR: In this paper, a Hessian-based predictor-corrector algorithm and a high-accuracy Hessian updating algorithm are described for enhancing the efficiency of direct dynamics simulations, in which an ensemble of trajectories is calculated which represents the experimental and chemical system under study.
Abstract: In classical and quasiclassical trajectory chemical dynamics simulations, the atomistic dynamics of collisions, chemical reactions, and energy transfer are studied by solving the classical equations of motion. These equations require the potential energy and its gradient for the chemical system under study, and they may be obtained directly from an electronic structure theory. This article reviews such direct dynamics simulations. The accuracy of classical chemical dynamics is considered, with simulations highlighted for the F− + CH3OOH reaction and of energy transfer in collisions of CO2 with a perfluorinated self-assembled monolayer (F-SAM) surface. Procedures for interfacing chemical dynamics and electronic structure theory computer codes are discussed. A Hessian-based predictor–corrector algorithm and high-accuracy Hessian updating algorithm, for enhancing the efficiency of direct dynamics simulations, are described. In these simulations, an ensemble of trajectories is calculated which represents the experimental and chemical system under study. Algorithms are described for selecting the appropriate initial conditions for bimolecular and unimolecular reactions, gas-surface collisions, and initializing trajectories at transition states and conical intersections. Illustrative direct dynamics simulations are presented for the Cl− + CH3I SN2 reaction, unimolecular decomposition of the epoxy resin constituent CH3NHCHCHCH3 versus temperature, collisions and reactions of N-protonated diglycine with a F-SAM surface that has a reactive head group, and the product energy partitioning for the post-transition state dynamics of C2H5F HF + C2H4 dissociation. © 2012 John Wiley & Sons, Ltd.
TL;DR: The report presents the possibility of utilizing NMR relaxation data, a more cost-effective experiment, to calculate internuclear distances in the case of drug-supramolecule complexes that are generally obtained by extremely time consuming two-dimensional nuclear Overhauser enhancement-based methods.
Abstract: The prime focus of the present study is to employ NMR relaxation measurement to address the intermolecular interactions, as well as motional dynamics, of drugs, viz., paracetamol and aspirin, encapsulated within the β-cyclodextrin (β-CD) cavity. In this report, we have attempted to demonstrate the applicability of nonselective (R1ns), selective (R1se), and bi-selective (R1bs) spin–lattice relaxation rates to infer dynamical parameters, for example, the molecular rotational correlation times (τc) and cross-relaxation rates (σij) of the encapsulated drugs. Molecular rotational correlation times of the free drugs were calculated using the selective relaxation rate in the fast molecular motion time regime (ωH2τc2 ≪ 1 and R1ns/R1se ≈ 1.500), whereas that of the 1:1 complexed drugs were found from the ratio of R1ns/R1se in the intermediate motion time regime (ωH2τc2 ∼ 1 and R1ns/R1se ≈ 1.054), and these values were compared with each other to confirm the formation of inclusion complexes. Furthermore, the cross-...
22 Jul 2019
TL;DR: The design and construction of versatile star-shaped intramolecular charge transfer (ICT) and ESIPT-active mechanoresponsive and aggregation-induced emissive (AIE) luminogen triaminoguanidine-diethylaminophenol (LH3) conjugate is reported, which exhibits mechanochromic fluorescence behavior upon external grinding.
Abstract: Design and development of multifunctional materials have drawn incredible attraction in recent years. Herein, we report the design and construction of versatile star-shaped intramolecular charge transfer (ICT)-coupled excited-state intramolecular proton transfer (ESIPT)-active mechanoresponsive and aggregation-induced emissive (AIE) luminogen triaminoguanidine-diethylaminophenol (LH3 ) conjugate from simple precursors triaminoguanidine hydrochloride and 4-(N,N-diethylamino)salicylaldehyde. Solvent-dependent dual emission in nonpolar to polar protic solvents implies the presence of ICT-coupled ESIPT features in the excited state. Aggregation-enhanced emissive feature of LH3 was established in the CH3CN/water mixture. Furthermore, this compound exhibits mechanochromic fluorescence behavior upon external grinding. Fluorescence microscopy images of pristine, crystal, and crushed crystals confirm the naked-eye mechanoresponsive characteristics of LH3 . In addition, LH3 selectively sensed a Cu2+ ion through a colorimetric and fluorescence "turn-off" route, and subsequently, the LH3 -Cu2+ ensemble could act as a selective and sensitive sensor for S2- in a "turn-on" fluorescence manner via a metal displacement approach. Reversible "turn-off-turn-on" features of LH3 with Cu2+/S2- ions were efficiently demonstrated to construct the IMPLICATION logic gate function. The Cu2+/S2--responsive sensing behavior of LH3 was established in the paper strip experiment also, which can easily be characterized by the naked eye under daylight as well as a UV lamp (λ = 365 nm).
TL;DR: Direct dynamics trajectory simulations were performed for two examples of the thiolate-disulfide exchange reaction, that is, HS(-) + HSSH and CH(3)S (-) + CH( 3)SSCH(3), where the mechanism is addition-elimination, with several trajectories sampling the intermediate for long times.
Abstract: Direct dynamics trajectory simulations were performed for two examples of the thiolate-disulfide exchange reaction, that is, HS(-) + HSSH and CH(3)S(-) + CH(3)SSCH(3). The trajectories were computed for the PBE0/6-31+G(d) potential energy surface using both classical microcanonical sampling at the ion-dipole complex and quasi-classical Boltzmann sampling (T = 300 K) at the central transition state. The potential energy surface for these reactions involves a hypercoordinate sulfur intermediate. Despite the fact that the intermediate resides in a shallow well (less than 5 kcal/mol), very few trajectories follow a direct substitution path (the S(N)2 pathway). Rather, the mechanism is addition-elimination, with several trajectories sampling the intermediate for long times, up to 15 ps or longer.
TL;DR: In the present work, unimolecular decomposition of formamide in the electronic ground state was investigated by classical direct chemical dynamics simulations using the density functional B3LYP/aug-cc-pVDZ level of electronic structure theory.
Abstract: Formamide (NH2CHO), being the simplest organic molecule containing an amide functional group, serves as a prototype to study protein and peptide chemistry. Formamide has been found in Comets and interstellar media and its decomposition results in smaller molecules such as NH3, CO, HCN, HNCO, etc. These smaller molecules are considered to have been potential precursors for the formation of complex biological molecules, such as nucleic acids and nucleobases, in the early Earth. Several experimental and theoretical investigations of formamide decomposition have been reported in the literature. In the present work, unimolecular decomposition of formamide in the electronic ground state was investigated by classical direct chemical dynamics simulations. The calculations were performed at three different energies using the density functional B3LYP/aug-cc-pVDZ level of electronic structure theory. The major dissociation products observed were NH3, CO, H2, HNCO, H2O, HCN, and HNC along with products of a few minor dissociation channels. Reactivity, atomic level mechanisms, and product branching ratios were investigated as a function of total energy.
01 Jan 1940
TL;DR: The intrinsic reaction coordinate (IRC) approach has been used extensively in quantum chemical analysis and prediction of the mechanism of chemical reactions as mentioned in this paper, which gives a unique connection from a given transition structure to local minima of the reactant and product sides.
Abstract: The intrinsic reaction coordinate (IRC) approach has been used extensively in quantum chemical analysis and prediction of the mechanism of chemical reactions. The IRC gives a unique connection from a given transition structure to local minima of the reactant and product sides. This allows for easy understanding of complicated multistep mechanisms as a set of simple elementary reaction steps. In this article, three topics concerning the IRC approach are discussed. In the first topic, the first ab initio study of the IRC and a recent development of an IRC calculation algorithm for enzyme reactions are introduced. In the second topic, cases are presented in which dynamical trajectories bifurcate and corresponding IRC connections can be inaccurate. In the third topic, a recent development of an automated reaction path search method and its application to systematic construction of IRC networks are described. Finally, combining these three topics, future perspectives are discussed. © 2014 Wiley Periodicals, Inc.
TL;DR: Using the nanoreactor, new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth are shown, providing new insight into the classic Urey-Miller experiment, highlighting the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings.
Abstract: Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings.
01 Feb 2014-Nature Chemistry
TL;DR: A system for which a single transition-state structure leads to the formation of many isomeric products via pathways that feature multiple sequential bifurcations is described, which redefine the challenges faced by nature in controlling the biosynthesis of complex natural products.
Abstract: A terpene-forming carbocation reaction is described for which a single transition-state structure leads to the formation of many isomeric products via pathways that feature multiple sequential bifurcations. Dynamic effects are shown to contribute to the selectivity of the reaction, with consequences for how enzymes control the biosynthesis of complex natural products.
TL;DR: Direct dynamics simulation studies are described for bimolecular SN2 nucleophilic substitution, unimolecular decomposition, post-transition-state dynamics, mass spectrometry experiments, and semiclassical vibrational spectra.
Abstract: In a direct dynamics simulation, the technologies of chemical dynamics and electronic structure theory are coupled so that the potential energy, gradient, and Hessian required from the simulation are obtained directly from the electronic structure theory. These simulations are extensively used to (1) interpret experimental results and understand the atomic-level dynamics of chemical reactions; (2) illustrate the ability of classical simulations to correctly interpret and predict chemical dynamics when quantum effects are expected to be unimportant; (3) obtain the correct classical dynamics predicted by an electronic structure theory; (4) determine a deeper understanding of when statistical theories are valid for predicting the mechanisms and rates of chemical reactions; and (5) discover new reaction pathways and chemical dynamics. Direct dynamics simulation studies are described for bimolecular SN2 nucleophilic substitution, unimolecular decomposition, post-transition-state dynamics, mass spectrometry experiments, and semiclassical vibrational spectra. Also included are discussions of quantum effects, the accuracy of classical chemical dynamics simulation, and the methodology of direct dynamics.