Non isothermal heat capacities and chemical reactions using a modulated DSC

An evaluation of measurements of heat capacities by modulated differential scanning calorimetry, MDSC is presented. Heat capacities were obtained from 130 to 550 K by a non isothermal technique in which a periodic modulation was added to the linear heating rate. Effects of amplitude and period of modulation, sample weight, sample type, pan type, and cell imbalance are described. Results are compared with those obtained using the isothermal technique. Heat capacity could be measured well into the decomposition region and separated from the non reversing signal due to chemical reaction (degradation), thus allowing a precise detection of onsets of the thermal degradation. This additional information will aid in the interpretation of the degradation chemistry, a field vital for the petroleum-industry.Dedicated to Professor Bernhard Wunderlich on the occasion of his 65th birthdayPart of this paper was presented at the 23rd Conference of the North American Thermal Analysis Society, Toronto, Canada, September 25–28, 1994.The author (MVN) acknowledges the experimental assistance provided by J. Balogh of Exxon Research and Engineering Company, Linden. Helpful discussions with A. Boller of the University of Tennessee at Knoxville, Dr. Y. Jin, General Electrical, and Dr. S. Sauerbrunn formerly of TA Instruments are also acknowledged.     

Kinetic Monte Carlo modeling of chemical reactions coupled with heat transfer

In this paper, we describe two types of effective events for describing heat transfer in a kinetic Monte Carlo (KMC) simulation that may involve stochastic chemical reactions. Simulations employing these events are referred to as KMC-TBT and KMC-PHE. In KMC-TBT, heat transfer is modeled as the stochastic transfer of "thermal bits" between adjacent grid points. In KMC-PHE, heat transfer is modeled by integrating the Poisson heat equation for a short time. Either approach is capable of capturing the time dependent system behavior exactly. Both KMC-PHE and KMC-TBT are validated by simulating pure heat transfer in a rod and a square and modeling a heated desorption problem where exact numerical results are available. KMC-PHE is much faster than KMC-TBT and is used to study the endothermic desorption of a lattice gas. Interesting findings from this study are reported.     

Predicting potentially hazardous chemical reactions using an explainable neural network

Predicting potentially dangerous chemical reactions is a critical task for laboratory safety. However, a traditional experimental investigation of reaction conditions for possible hazardous or explosive byproducts entails substantial time and cost, for which machine learning prediction could accelerate the process and help detailed experimental investigations. Several machine learning models have been developed which allow the prediction of major chemical reaction products with reasonable accuracy. However, these methods may not present sufficiently high accuracy for the prediction of hazardous products which particularly requires a low false negative result for laboratory safety in order not to miss any dangerous reactions. In this work, we propose an explainable artificial intelligence model that can predict the formation of hazardous reaction products in a binary classification fashion. The reactant molecules are transformed into substructure-encoded fingerprints and then fed into a convolutional neural network to make the binary decision of the chemical reaction. The proposed model shows a false negative rate of 0.09, which can be compared with 0.47–0.66 using the existing main product prediction models. To provide explanations for what substructures of the given reactant molecules are important to make a decision for target hazardous product formation, we apply an input attribution method, layer-wise relevance propagation, which computes the contributions of individual inputs per input data. The computed attributions indeed match some of the existing chemical intuitions and mechanisms, and also offer a way to analyze possible data-imbalance issues of the current predictions based on relatively small positive datasets. We expect that the proposed hazardous product prediction model will be complementary to existing main product prediction models and experimental investigations.

An explainable neural network model is developed to predict the formation of hazardous products for chemical reactions. An input attribution method, layer-wise relevance propagation, is used to explain the decision-making process.     

Peripheral chemical reactions

Forward scattering of the products of direct exoergic atom transfer reactions is proposed as an indication for a peripheral attraction: a reaction in which an atom at the periphery of the reactants is abstracted. Model computations for the O(¹D) + N₂O reaction are used to illustrate the proposed mechanism. The opacity function has a peak at higher impact parameters which is correlated with the forward scattering. Potential energy surfaces which do not manifest peripheral attraction lead to backwards scattering of the products.     

Modular approach to functional hyaluronic acid hydrogels using orthogonal chemical reactions

A modular approach for the synthesis of hyaluronic acid hydrogels using orthogonal chemoselective reactions for subsequent enzymatic decomposition to nanoparticles is described.     

Conditions for calibration of an isothermal titration calorimeter using chemical reactions

The reaction of protonation of 2-amino-2-(hydroxymethyl)-1,3-propanediol (TRIS) is a suitable one for the calibration of isothermal titration calorimeter (ITC), providing that experimental conditions are appropriately chosen. The conditions and methods for handling experimental data from a nanowatt-ITC are discussed. Also, the binding of Ba²⁺ to 18-Crown-6 is successfully used to check the accuracy and precision of the chemical calibration performed with TRIS. This latter reaction has the additional advantage that the data can also be used for a check on the determination of the value of a binding constant. The anomaly of the first injection in ITC is analyzed and, by combining calorimetric and spectroscopic measurements, it is shown that it mainly results from a backlash effect of the syringe plunger rather than from a diffusion effect.     

Identification of decomposition reactions for HMDSO organosilicon using quantum chemical calculations

Hexamethyldisiloxane [HMDSO, (CH₃)₃-SiOSi-(CH₃)₃] is an important precursor for SiO₂ formation during flame-based silica material synthesis. As a result, HMDSO reactions in flame have been widely investigated experimentally, and many results have indicated that HMDSO decomposition reactions occur very early in this process. In this paper, quantum chemical calculations are performed to identify the initial decomposition of HMDSO and its subsequent reactions using the density functional theory at the level of B3LYP/6-311+G (d, p). Four reaction pathways—(a) Si O bond dissociation of HMDSO, (b) Si C bond dissociation of HMDSO, (c) dissociation and recombination of Si O and Si C bonds, and (d) elimination of a methane molecule from HMDSO—have been examined and identified. From the results, it is found that the barrier of 84.38 kcal/mol and Si O bond dissociation energy of 21.55 kcal/mol are required for the initial decomposition reaction of HMDSO in the first pathway, but the highest free energy barrier (100.69 kcal/mol) is found in the third reaction pathway. By comparing the free energy barriers and reaction rate constants, it is concluded that the most possible initial decomposition reaction of HMDSO is to eliminate the CH₃ radical by Si C bond dissociation.     

Observing the stereodynamics of chemical reactions using randomly oriented molecular beams

A new method is demonstrated to study the stereodynamics of simple chemical reactions that does not require the use of oriented (or aligned) molecular beams or measurements of the orientation state of product molecules. Instead, it is shown that by numerically combining accurate measurements of the state-to-state differential cross section for two or more rotational states of the reagent molecule, the separate contribution from the individual helicity states can be extracted. New molecular beam experiments are conducted for the D+H(2)-->HD+H reaction that confirm the validity of the method.     

Independence of chemical reactions

Up to this time the existence of physically true dependences between elementary reactions has been a returning question. The goal of this paper is to show that the real elementary reactions of a mechanism are practically independent. Introducing the concept of the space-time volume of a reaction (the reciprocal of the reaction rate) it is shown that, except for extremely fast processes (explosions), the reactions form very dilute systems. This systems must be ideal in the sense that interactions between elementary processes are very rare. The system exhibits some analogies with a dilute gas or solution. The extents of interactions can be calculated and the limits of independence estimated in this way.

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Monitoring of chemical reactions within microreactors using an inverted Raman microscopic spectrometer

An inverted Raman microscope spectrometer has been used to profile the spatial evolution of reactant and product concentrations for a chemical reaction within a microreactor operating under hydrodynamic flow control. The Raman spectrometer was equipped with a laser source at wavelength of 780 nm, confocal optics, a holographic transmission grating, and a charge-coupled device (CCD) detector. The microreactor consisted of a T-shaped channel network etched within a 0.5 mm thick glass bottom plate that was thermally bonded to a 0.5 mm thick glass top plate. The ends of the channel network were connected to reagent reservoirs that were linked to a syringe pump for driving the solutions by hydrodynamic pumping within the channels. The microchannels were 221 micro m wide and 73 micro m deep. The synthesis of ethyl acetate from ethanol and acetic acid was investigated as a model system within the microreactor as Raman scattering bands for each reactant and product species were clearly resolved. Raman spectral intensities of each band were proportional to concentration for each species and hence all concentrations could be quantitatively measured after calibration. By scanning specific Raman bands within a selected area in the microchannel network at given steps in the X-Y plane, spatially resolved concentration profiles were obtained under steady-state flow conditions. Under the flow conditions used, different positions within the concentration profile correspond to different times after contact and mixing of the reagents, thereby enabling one to observe the time dependence of the product formation. Raman microscopy provides a useful complementary technique to UV/VIS absorbance and fluorescence methods for the in situ monitoring and analysis of chemical reaction species having their lowest S(0)-S(1) absorption bands too far in the UV to be of use, due to their probable overlap with the bands from other reactant, product and solvent molecules.     

Lossless compression of chemical fingerprints using integer entropy codes improves storage and retrieval

Many modern chemoinformatics systems for small molecules rely on large fingerprint vector representations, where the components of the vector record the presence or number of occurrences in the molecular graphs of particular combinatorial features, such as labeled paths or labeled trees. These large fingerprint vectors are often compressed to much shorter fingerprint vectors using a lossy compression scheme based on a simple modulo procedure. Here, we combine statistical models of fingerprints with integer entropy codes, such as Golomb and Elias codes, to encode the indices or the run lengths of the fingerprints. After reordering the fingerprint components by decreasing frequency order, the indices are monotone-increasing and the run lengths are quasi-monotone-increasing, and both exhibit power-law distribution trends. We take advantage of these statistical properties to derive new efficient, lossless, compression algorithms for monotone integer sequences: monotone value (MOV) coding and monotone length (MOL) coding. In contrast to lossy systems that use 1024 or more bits of storage per molecule, we can achieve lossless compression of long chemical fingerprints based on circular substructures in slightly over 300 bits per molecule, close to the Shannon entropy limit, using a MOL Elias Gamma code for run lengths. The improvement in storage comes at a modest computational cost. Furthermore, because the compression is lossless, uncompressed similarity (e.g., Tanimoto) between molecules can be computed exactly from their compressed representations, leading to significant improvements in retrival performance, as shown on six benchmark data sets of druglike molecules.     

Superlinear scaling in master-slave quantum chemical calculations using in-core storage of two-electron integrals

We describe the implementation of a parallel, in-core, integral-direct Hartree-Fock and density functional theory code for the efficient calculation of Hartree-Fock wave functions and density functional theory. The algorithm is based on a parallel master-slave algorithm, and the two-electron integrals calculated by a slave are stored in available local memory. To ensure the greatest computational savings, the master node keeps track of all integral batches stored on the different slaves. The code can reuse undifferentiated two-electron integrals both in the wave function optimization and in the evaluation of second-, third-, and fourth-order molecular properties. Superlinear scaling is achieved in a series of test examples, with speedups of up to 55 achieved for calculations run on medium-sized molecules on 16 processors with respect to the time used on a single processor.     

Laser control of chemical reactions

Chemical reactions are at the heart of chemistry and the dream of controlling the outcome of these reactions is an old one. Thus, with given reactants, a solvent and perhaps assisted by a catalyst, we would like to 'steer' the reactants into a particular desired product. This review focuses on how to control the dynamics of chemical reactions, beyond traditional temperature control, with the emphasis on unimolecular reactions. The electromagnetic radiation of lasers can induce so-called coherent dynamics. The recent theoretical and experimental results on this coherent control are explained and illustrated with computational and experimental examples.     

Geometric description of chemical reactions

We use the formalism of Geometrothermodynamics to describe chemical reactions in the context of equilibrium thermodynamics. Any chemical reaction in a closed system is shown to be described by a geodesic in a 2-dimensional manifold that can be interpreted as the equilibrium space of the reaction. We first show this in the particular cases of a reaction with only two species corresponding to either two ideal gases or two van der Waals gases. We then consider the case of a reaction with an arbitrary number of species. The initial equilibrium state of the geodesic is determined by the initial conditions of the reaction. The final equilibrium state, which follows from a thermodynamic analysis of the reaction, is shown to correspond to a coordinate singularity of the thermodynamic metric which describes the equilibrium manifold.     

Dynamics of nonadiabatic chemical reactions

New methods are proposed to treat nonadiabatic chemical dynamics in realistic large molecular systems by using the Zhu-Nakamura (ZN) theory of curve-crossing problems. They include the incorporation of the ZN formulas into the Herman-Kluk type semiclassical wave packet propagation method and the trajectory surface hopping (TSH) method, formulation of the nonadiabatic transition state theory, and its application to the electron transfer problem. Because the nonadiabatic coupling is a vector in multidimensional space, the one-dimensional ZN theory works all right. Even the classically forbidden transitions can be correctly treated by the ZN formulas. In the case of electron transfer, a new formula that can improve the celebrated Marcus theory in the case of normal regime is obtained so that it can work nicely in the intermediate and strong electronic coupling regimes. All these formulations mentioned above are demonstrated to work well in comparison with the exact quantum mechanical numerical solutions and are expected to be applicable to large systems that cannot be treated quantum mechanically numerically exactly. To take into account another quantum mechanical effect, namely, the tunneling effect, an efficient method to detect caustics from which tunneling trajectories emanate is proposed. All the works reported here are the results of recent activities carried out in the author's research group. Finally, the whole set of ZN formulas is presented in Appendix.