Some formal properties of the density matrix

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.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/qua.24757

Intrinsic reaction coordinate: Calculation, bifurcation, and automated search

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.

/pdf/discovering-chemistry-with-an-ab-initio-nanoreactor-1v1zz669b4.pdf

Discovering chemistry with an ab initio nanoreactor

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.

Biosynthetic consequences of multiple sequential post-transition-state bifurcations

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.

Direct Chemical Dynamics Simulations.

The role of second-order saddle in the isomerization dynamics was investigated by considering the $$E-Z$$
 isomerization of guanidine. The potential energy profile for the reaction was mapped using the ab initio wavefunction method. The isomerization path involved a torsional motion about the imine (C-N) bond in a clockwise or an anticlockwise fashion resulting in two degenerate transition states corresponding to a barrier of 23.67 kcal/mol.
An alternative energetically favorable path (
 $$\sim$$
 1 kcal/mol higher than the transition states) by an in-plane motion of the imine (N-H) bond via a second-order saddle point on the potential energy surface was also obtained. The dynamics of the isomerization was investigated by ab initio classical trajectory simulations. The trajectories reveal that isomerization happens via the transition states as well as the second-order saddle. The dynamics was found to be nonstatistical with trajectories exhibiting recrossing and the higher energy second-order saddle pathway preferred over the traditional transition state pathway. Wavelet based time-frequency analysis of internal coordinates indicate regular dynamics and existence of long-lived quasi-periodic trajectories in the phase space.

Second-order Saddle Dynamics in Isomerization Reaction

Formation of simple organic species such as glycine in the interstellar medium and transportation to earth via meteorites is considered to be a possible route for ‘Origin of Life’ on earth. Glycine formation has been proposed to occur via two different pathways involving formaldehyde (
 $$\hbox {HCHO}$$
 ) and methanimine (
 $$\hbox {CH}_{2} = \hbox {NH}$$
 ) as key intermediates. In the second pathway, which is the topic of this paper, $$\hbox {CH}_{2} = \hbox {NH}$$
 reacts with $$\hbox {CO}$$
 and $$\hbox {H}_{2} \hbox {O}$$
 forming neutral glycine. In a recent article (Nhlabatsi et al. in Phys. Chem. Chem. Phys. 18:375, 2016), detailed electronic structure calculations were reported for the reaction between $$\hbox {CH}_{2} = \hbox {NH}$$
 , $$\hbox {CO}$$
 and $$(\hbox {H}_{2} \hbox {O})_n$$
 , $$n = 1, 2, 3$$
 , and 4, forming glycine in the interstellar media. The presence of additional water molecule(s) for this reaction reduces reaction barrier - thus exhibiting a catalytic effect. This effect was described in terms of efficient proton transfer mediated by the additional water molecule through a relay transport mechanism. In the present article, we report ab initio classical trajectory simulations for the interstellar formation of glycine for the above mentioned reaction with $$n = 1$$
 and 2. The trajectories were generated on-the-fly over a density functional B3LYP/6-31++G(3df,2pd) potential energy surface. Our simulations indicate that the above proposed catalytic effect by the additional water molecule(s) may not be a classical effect. Synopsis: Glycine formation in the interstellar media via the $$\hbox {CH}_{2} = \hbox {NH} + \hbox {CO} + \hbox {H}_{2} \hbox {O}$$
 reaction was investigated by classical chemical dynamics simulations. This reaction has a large barrier which reduces in presence of additional water molecules. Our simulations indicate that the proposed catalytic effect by the additional water molecules may not be a classical effect.

/pdf/classical-dynamics-simulations-of-interstellar-glycine-2g5jocnpvp.pdf

Classical dynamics simulations of interstellar glycine formation via $$\hbox {CH}_{2} = \hbox {NH} + \hbox {CO} + \hbox {H}_{2}\hbox {O}$$ reaction

3-Oxetanone is a strained cyclic molecule which plays an important role in synthetic chemistry. A few studies exist in the literature about the equilibrium properties of this molecule and the dissociation patterns of substituted 3-oxetanones. For the unsubstituted 3-oxetanone, formation of ketene (CH2CO) and formaldehyde (HCHO) was considered to be the major dissociation pathway. In a recent work, pyrolysis products of 3-oxetanone molecule in the gas phase were investigated by Fourier transform infrared spectroscopy and photoionization mass spectrometry. In this study, an additional dissociation channel forming ethylene oxide (c-C2H4O) and carbon monoxide CO was reported. In the present work, gas phase dissociation chemistry of 3-oxetanone was investigated by electronic structure theory, ab initio classical chemical dynamics simulations, and Rice–Ramsperger–Kassel–Marcus (RRKM) rate constant calculations. The barrier height for the ethylene oxide channel was found to be much higher than the ketene pathway...

Dissociation Chemistry of 3-Oxetanone in the Gas Phase.

Halogen substituted analogues of formaldehyde, HXCO (X = F, Cl, Br, and I), play a crucial role in the degradation of stratospheric ozone. Several spectroscopic and quantum chemistry investigations of the dissociation chemistry of formyl halides have been reported in the literature. Due to their importance in combustion and atmospheric chemistry, we investigated the gas phase dissociation of formyl halides using electronic structure theory, direct chemical dynamics simulations, and Rice–Ramsperger–Kassel–Marcus rate constant calculations. Chemical dynamics simulations were performed using density functional B3LYP/6-31G* theory with suitable effective core potentials for the halogen atoms. Simulations showed multiple pathways and mechanisms for the dissociation of formyl halides. The major reaction products were HX + CO which formed via direct and indirect pathways. Trajectory lifetime distribution calculations indicated non-statistical dissociation dynamics.

Theoretical investigation of the dissociation chemistry of formyl halides in the gas phase.

Two important methods for enhancing gas sensing performance are vacancy/defect and interlayer engineering. Tin sulfide (SnS2) has recently attracted much attention for sensing of the NO2 gas due to its active surface sites and tunable electronic structure. Herein, SnS2 has been synthesized by the chemical vapor deposition (CVD) method followed by nitrogen plasma treatment with different exposure times for fast detection of NO2 molecules. Plasma treatment created a substantial number of surface vacancies on SnS2 flakes, which were controlled by the exposure period to modify the surface of flakes. After 12 min of nitrogen plasma treatment, SnS2 nanoflakes show considerable improvement in NO2 sensing characteristics, including a high sensing response of ∼264% toward 100 ppm NO2 at 120°C. The enhancement in the relative response of the sensor is due to the electronic interaction between NO2 molecules and the S vacancies on the surface of SnS2. Density functional theory (DFT) computations indicate that the S-vacancy defects on the surface dominate the effective NO2 detection and the NO2 adsorption mechanism transition from physisorption to chemisorption. Adsorption kinetics of the NO2 gas over SnS2 nanoflake-based chemiresistor sensors were studied using the Lee and Strano model [ Langmuir 2005, 21(11), 5192-5196]. The irreversible rate of the reaction for various NO2 concentrations exposed to the gas sensor is extracted using this model, which also appropriately describes the response curves. The forward rate constant of the irreversible gas sensor increased with the increase of the N2 plasma treatment time and reached the maximum in the 12 min plasma-treated sample. Through defect engineering, this research may open up new vistas for the design and synthesis of 2D materials with enhanced sensing properties.

Manikandan Paranjothy

Papers

Second-order Saddle Dynamics in Isomerization Reaction

Classical dynamics simulations of interstellar glycine formation via $$\hbox {CH}_{2} = \hbox {NH} + \hbox {CO} + \hbox {H}_{2}\hbox {O}$$ reaction

Dissociation Chemistry of 3-Oxetanone in the Gas Phase.

Theoretical investigation of the dissociation chemistry of formyl halides in the gas phase.

Investigations of Vacancy-Assisted Selective Detection of NO2 Molecules in Vertically Aligned SnS2.