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Porphyrins and amino acids chemical bonding under geochemically plausible conditions, considering diagenesis of biogenic compounds and life processes prebiotic chemical evolution
An important goal of quantum chemical calculations is to provide an understanding of chemical bonding and molecular electronic structure. A second goal, the prediction of energy differences to chemical accuracy, has been much harder to attain. First, the computational resources required to achieve such accuracy are very large, and second, it is not straightforward to demonstrate that an apparently accurate result, in terms of agreement with experiment, does not result from a cancellation of errors. Recent advances in electronic structure methodology, coupled with the power of vector supercomputers, have made it possible to solve a number of electronic structure problems exactly using the full configuration interaction (FCI) method within a subspace of the complete Hilbert space. These exact results can be used to benchmark approximate techniques that are applicable to a wider range of chemical and physical problems. The methodology of many-electron quantum chemistry is reviewed. Methods are considered in detail for performing FCI calculations. The application of FCI methods to several three-electron problems in molecular physics are discussed. A number of benchmark applications of FCI wave functions are described. Atomic basis sets and the development of improved methods for handling very large basis sets are discussed: these are then applied to a number of chemical and spectroscopic problems; to transition metals; and to problems involving potential energy surfaces. Although the experiences described give considerable grounds for optimism about the general ability to perform accurate calculations, there are several problems that have proved less tractable, at least with current computer resources, and these and possible solutions are discussed.
The goal of this work is to identify the spectral signature of chemisorbed CO2, to test the efficacy of carbonate formation on Mars-analog materials via CO2 chemisorption, and to identify the surface-chemical characteristics of good chemisorbents, with the intent of assessing the possible geochemical importance of CO2 chemisorption as a quasipermanent CO2 sink in the Martian environment. Our approach is to search for infrared spectral bands that result from chemisorption of CO2 molecules onto chemical reagents and Mars-analog materials, and to identify the salient differences in adsorbents that favor strong, permanent CO2 chemisorption. The total amount of CO2 in the early Martian atmosphere, and consequent surface temperatures, are unknown. A CO2 greenhouse may not have been an adequate mechanism under any circumstances; however, it if were, then most of that CO2 must still be in the near-surface environment; no escape mechanism that could remove it after the decline of channeling has been identified. The only plausible reservoir is carbonate, and there are various remote sensing techniques that can be used to search for it. We are investigating CO2 chemisorption as a permanent CO2 sink, and to aid in interpretation of remotely sensed IR spectra of Mars. A common effect reported in CO2 adsorption studies is the formation of a layer of carbonate or bicarbonate anions on adsorbents that have OH- groups available on their surfaces. Inorganic hydroxyls occur on phyllosilicates, amorphous silicates, metal oxides and hydroxides; it is the most abundant and reactive surface functional group on the surfaces of terrestrial silicates. The process responsible for the reaction is chemisorption. Chemisorption is distinguished from physical adsorption in that there is a transfer of electrons between species, and the formation of a chemical bond. The heat of chemisorption is typically of the same order as heats of chemical reaction (i.e., a few hundred to a few thousand kJ/mole), as opposed to heats of physical adsorption (a few kJ per mole). Chemisorption is an activated process that is promoted by an increase in temperature - quite the opposite of physical adsorption. Chemisorption is not reversible in the sense that physical adsorption is.
The nature of the bonding of a nanotube is described by applied quantum chemistry, specifically, orbital hybridization. The chemical bonding of nanotubes is composed entirely of sp2 bonds, similar to those of graphite. This bonding structure, which is stronger than the sp3 bonds found in diamonds, provides the molecules with their unique strength. Nanotubes naturally align themselves into "ropes" held together by Van der Waals forces. Under high pressure, nanotubes can merge together, trading some sp² bonds for sp³ bonds, giving the possibility of producing strong, unlimited-length wires through high-pressure nanotube linking. This document looks at the topic of carbon nanotubes as it applies to microelectronics packaging and assembly.
Molecular dynamics simulations are used to study the mechanical degradation of well-entangled polymer melts during uniaxial extensional flow. Simulations measure the transient rise in extensional stresses and relate them to the molecular alignment and scission of chain backbones. Intermolecular entanglements couple chain scission in space and time, making degradation sensitive to deformation history and strain rate in ways not displayed by dilute polymer solutions. The rate of chain scission is nonmonotonic and peaks at strains corresponding to the maximum extensibility of entanglement segments but prior to the full extension of chain backbones. We measure a specific work per scission event w* and decompose it into separate contributions associated with chain alignment, chemical bond breaking, and scission-induced plasticity. We find chain scission in melts requires activating plastic dissipation that is multiple orders of magnitude larger than the chemical work required to break a covalent backbone bond. Our findings underscore the critical need to consider bulk polymer mechanics and rheology in designing efficient mechanical degradation and mechanochemical processes.
Abstract Surface functionalization of two‐dimensional crystals is a key path to tuning their intrinsic physical and chemical properties. However, synthetic protocols and experimental strategies to directly probe chemical bonding in modified surfaces are scarce. Introduced herein is a mild, surface‐specific protocol for the surface functionalization of few‐layer black phosphorus nanosheets using a family of photolytically generated nitrenes (RN) from the corresponding azides. By embedding spectroscopic tags in the organic backbone, a multitude of characterization techniques are employed to investigate in detail the chemical structure of the modified nanosheets, including vibrational, X‐ray photoelectron, solid state 31 P NMR, and UV‐vis spectroscopy. To directly probe the functional groups introduced on the surface, R fragments were selected such that in conjunction with vibrational spectroscopy, 15 N‐labeling experiments, and DFT methods, diagnostic P=N vibrational modes indicative of iminophosphorane units on the nanosheet surface could be conclusively identified.
Abstract Several renewable energy schemes aim to use the chemical bonds in abundant molecules like water and ammonia as energy reservoirs. Because the O-H and N-H bonds are quite strong (>100 kcal/mol), it is necessary to identify substances that dramatically weaken these bonds to facilitate proton-coupled electron transfer processes required for energy conversion. Usually this is accomplished through coordination-induced bond weakening by redox-active metals. However, coordination-induced bond weakening is difficult with earth’s most abundant metal, aluminum, because of its redox inertness under mild conditions. Here, we report a system that uses aluminum with a redox non-innocent ligand to achieve significant levels of coordination-induced bond weakening of O-H and N-H bonds. The multisite proton-coupled electron transfer manifold described here points to redox non-innocent ligands as a design element to open coordination-induced bond weakening chemistry to more elements in the periodic table.
The bonding of two materials through hydroxide-catalyzed hydration/dehydration is achieved at room temperature by applying hydroxide ions to at least one of the two bonding surfaces and by placing the surfaces sufficiently close to each other to form a chemical bond between them. The surfaces may be placed sufficiently close to each other by simply placing one surface on top of the other. A silicate material may also be used as a filling material to help fill gaps between the surfaces caused by surface figure mismatches. A powder of a silica-based or silica-containing material may also be used as an additional filling material. The hydroxide-catalyzed bonding method forms bonds which are not only as precise and transparent as optical contact bonds, but also as strong and reliable as high-temperature frit bonds. The hydroxide-catalyzed bonding method is also simple and inexpensive.
A project to investigate space environment effects on specific materials with interest to remote sensing was initiated in 2016. The goal of the project is to better characterize changes in the optical properties of polymers and Mylar, specifically those found in multi-layered spacecraft insulation, due to electron bombardment. Previous analysis shows that chemical bonds break and potentially reform when exposed to high energy electrons. Among other properties these chemical changes altered the optical reflectance as documented in laboratory analysis. This paper presents results of the initial experiment results focused on the exposure of materials to various fluences of high energy electrons, used to simulate a portion of the geosynchronous space environment. The paper illustrates how the spectral reflectance changes as a function of time on orbit with respect to GEO environmental factors and investigates the survivability of the material after multiple electron doses. These results provide a baseline for analysis of aging effects on satellite systems used for remote sensing. They also provide preliminary analysis on what materials are most likely to encompass the high area-to-mass population of space debris in the geosynchronous environment. Lastly, the paper provides the results of the initial experimentation as a proof of concept for space aging on polymers and Mylar for conducting more experiments with a larger subset of spacecraft materials.
Diamond shows unprecedented hardness. Because hardness is a measure of resistance of chemical bonds in a material to external indentation, the electronic bonding nature of diamond beyond several million atmospheres is key to understanding the origin of hardness. However, probing the electronic structures of diamond at such extreme pressure has not been experimentally possible. The measurements on the inelastic x-ray scattering spectra for diamond up to 2 million atmospheres provide data on the evolution of its electronic structures under compression. The mapping of the observed electronic density of states allows us to obtain a two-dimensional image of the bonding transitions of diamond undergoing deformation. The spectral change near edge onset is minor beyond a million atmospheres, while its electronic structure displays marked pressure-induced electron delocalization. Such electronic responses indicate that diamond’s external rigidity is supported by its ability to reconcile internal stress, providing insights into the origins of hardness in materials.
This X-ray photoemission (XPS) study demonstrates a correlation of intrinsic TM-Si chemical bond formation with Schottky barrier heights for the near-noble transition metals (TM = Ni, Pd, Pt) and their corresponding silicides (TM2Si and TMSi) on Si(100). It is found that the barrier height correlates with the strength of the TM-Si orbital interaction as well as with the charge density around the Si atom. These observations suggest a dominant role for intrinsic chemical interactions in establishing the Schottky barrier heights in these TM-Si systems.
In the field of metabolomics, mass spectrometry (MS) is the method most commonly used for identifying and annotating metabolites. As this typically involves matching a given MS spectrum against an experimentally acquired reference spectral library, this approach is limited by the coverage and size of such libraries (which typically number in the thousands). These experimental libraries can be greatly extended by predicting the MS spectra of known chemical structures (which number in the millions) to create computational reference spectral libraries. To facilitate the generation of predicted spectral reference libraries we developed CFM-ID, a computer program that can accurately predict ESI-MS/MS spectrum for a given compound structure. CFM-ID is one of the best-performing methods for compound-to-mass-spectrum prediction, and also one of the top tools for in silico mass-spectrum-to-compound identification. This work improves CFM-ID’s ability to predict ESI-MS/MS spectra from compounds by: (1) learning parameters from features based on the molecular topology, (2) adding a new approach to ring cleavage that models such cleavage as a sequence of simple chemical bond dissociations and (3) expanding its hand-written rule-based predictor to cover more chemical classes, including acylcarnitines, acylcholines, flavonols, flavones, flavanones, and flavonoid glycosides. We demonstrate that this new version of CFM-ID (version 4.0) is significantly more accurate than previous CFM-ID versions, in terms of both EI-MS/MS spectral prediction and compound identification. CFM-ID 4.0 is available at http://cfmid4.wishartlab.com/ as a webservice and docker images can be downloaded at https://hub.docker.com/r/wishartlab/cfmid
“Spacecraft potable water systems require a biocidal agent that effectively provides both immediate and residual disinfection over long periods of time. Ionic silver (Ag+) is a leading candidate for this application, but suffers from rapid concentration loss due to interactions with the metal storage containers and tubing. In order to maintain biocidal efficacy in systems with long periods of dormancy and to reduce the required rate of Ag+ injection, it is necessary to develop alternative materials and coatings for certified metal alloys that significantly reduce the Ag+loss.”1In this work, we continue our investigation of vapor-deposited parylene (AF4, and now C) polymers as conformal barrier coatings under long-term (ca. 1-year) immersion in ca. 400 ppb Ag+. The performanceof internal coatings in tubing/two-ferrule fitting systems is characterized. We report successful “aging” and high concentration Ag+pretreatment of parylene coatings for quantitative reduction of Ag+loss rates. In addition, we observe long-term blister-free adhesion of mechanically anchored parylene-AF4 on nano-structured Ti-6Al-4V alloy and chemically bonded parylene-C on 316L stainless steel. Finally, we report preliminary experiments with mechanical and chemical anchoring of laboratory-deposited parylene-C on 316L.
Bond dissociation energetics underpin the thermodynamics of chemical transformations where bonds are broken or formed and can also be used to predict reaction rates and selectivities.
A project to investigate space environment effects on specific materials with interest to remote sensing was initiated in 2016. The goal of the project is to better characterize changes in the optical properties of polymers found in multi-layered spacecraft insulation (MLI) induced by electron bombardment. Previous analysis shows that chemical bonds break and potentially reform when exposed to high energy electrons like those seen in orbit. These chemical changes have been shown to alter a material's optical reflectance, among other material properties. This paper presents the initial experimental results of MLI materials exposed to various fluences of high energy electrons, designed to simulate a portion of the geosynchronous Earth orbit (GEO) space environment. It is shown that the spectral reflectance of some of the tested materials changes as a function of electron dose. These results provide an experimental benchmark for analysis of aging effects on satellite systems which can be used to improve remote sensing and space situational awareness. They also provide preliminary analysis on those materials that are most likely to comprise the high area-to-mass ratio (HAMR) population of space debris in the geosynchronous orbit environment. Finally, the results presented in this paper serve as a proof of concept for simulated environmental aging of spacecraft polymers that should lead to more experiments using a larger subset of spacecraft materials.
TurboRVB is a computational package for ab initio Quantum Monte Carlo (QMC) simulations of both molecular and bulk electronic systems. The code implements two types of well established QMC algorithms: Variational Monte Carlo (VMC) and diffusion Monte Carlo in its robust and efficient lattice regularized variant. A key feature of the code is the possibility of using strongly correlated many-body wave functions (WFs), capable of describing several materials with very high accuracy, even when standard mean-field approaches [e.g., density functional theory (DFT)] fail. The electronic WF is obtained by applying a Jastrow factor, which takes into account dynamical correlations, to the most general mean-field ground state, written either as an antisymmetrized geminal power with spin-singlet pairing or as a Pfaffian, including both singlet and triplet correlations. This WF can be viewed as an efficient implementation of the so-called resonating valence bond (RVB) Ansatz, first proposed by Pauling and Anderson in quantum chemistry [L. Pauling, The Nature of the Chemical Bond (Cornell University Press, 1960)] and condensed matter physics [P.W. Anderson, Mat. Res. Bull 8, 153 (1973)], respectively. The RVB Ansatz implemented in TurboRVB has a large variational freedom, including the Jastrow correlated Slater determinant as its simplest, but nontrivial case. Moreover, it has the remarkable advantage of remaining with an affordable computational cost, proportional to the one spent for the evaluation of a single Slater determinant. Therefore, its application to large systems is computationally feasible. The WF is expanded in a localized basis set. Several basis set functions are implemented, such as Gaussian, Slater, and mixed types, with no restriction on the choice of their contraction. The code implements the adjoint algorithmic differentiation that enables a very efficient evaluation of energy derivatives, comprising the ionic forces. Thus, one can perform structural optimizations and molecular dynamics in the canonical NVT ensemble at the VMC level. For the electronic part, a full WF optimization (Jastrow and antisymmetric parts together) is made possible, thanks to state-of-the-art stochastic algorithms for energy minimization. In the optimization procedure, the first guess can be obtained at the mean-field level by a built-in DFT driver. The code was efficiently parallelized by using a hybrid MPI-OpenMP protocol, which is also an ideal environment for exploiting the computational power of modern Graphics Processing Unit accelerators.
Abstract The harpoon mechanism has been a milestone in molecular reaction dynamics. Until now, the entity from which electron harpooning occurs has been either alkali metal atoms or non‐metallic analogs in their excited states. In this work, we demonstrate that a common organic molecule, octamethylcalix[4] pyrrole (omC4P), behaves just like alkali metal atoms, enabling the formation of charge‐separated ionic bonding complexes with halogens omC4P + ⋅ X − ( X =F−I, SCN) via the harpoon mechanism. Their electronic structures and chemical bonding were determined by cryogenic photoelectron spectroscopy of the corresponding anions and confirmed by theoretical analyses. The omC4P + ⋅ X − could be visualized to form from the reactants omC4P+ X via electron harpooning from omC4P to X at a distance defined by the energy difference between the ionization potential of omC4P and electron affinity of X .
Development of efficient carbon capture-and-release technologies with minimal energy input is a long-term challenge in mitigating CO 2 emissions, especially via CO 2 chemisorption driven by engineered chemical bond construction. Herein, taking advantage of the structural diversity of ionic liquids (ILs) in tuning their physical and chemical properties, precise reaction energy regulation of CO 2 chemisorption was demonstrated deploying metal-ion-amino-based ionic liquids (MAILs) as absorbents. The coordination ability of different metal sites (Cu, Zn, Co, Ni, and Mg) to amines was harnessed to achieve fine-tuning on stability constants of the metal ion-amine complexes, acting as the corresponding cations in the construction of diverse ILs coupled with CO 2 -philic anions. The as-afforded MAILs exhibited efficient and controllable CO 2 release behavior with great reduction in energy input and minimal sacrifice on CO 2 uptake capacity. This coordination-regulated approach offers new prospects for the development of ILs-based systems and beyond towards energy-efficient carbon capture technologies.