A mechanism of abiogenesis based on complex reaction networks organized by seed-dependent autocatalytic systems

The core of the origin-of-life problem is to explain how a complex dissipative system could emerge spontaneously from a simple environment, perpetuate itself, and complexify over time. This would only be possible, we argue, if prebiotic chemical reaction networks had autocatalytic features organized in a way that permitted the accretion of complexity even in the absence of genetic control. To evaluate this claim, we developed tools to analyze the autocatalytic organization of food-driven reaction networks and applied these tools to both abiotic and biotic networks. Both networks contained seed-dependent autocatalytic systems (SDASs), which are subnetworks that can use a flux of food chemicals to self-propagate if, and only if, they are first seeded by some non-food chemicals. Moreover, SDASs were organized such that the activation of a lower-tier SDAS could render new higher-tier SDASs accessible. The organization of SDASs is, thus, similar to trophic levels (producer, primary consumer, etc.) in a biological ecosystem. Furthermore, similar to ecological succession, we found that higher-tier SDASs may produce chemicals that enhance the ability of the entire chemical ecosystem to utilize food more efficiently. The SDAS concept explains how driven abiotic environments, namely ones receiving an ongoing flux of food chemicals, can incrementally complexify even without genetic polymers. This framework predicts that it ought to be possible to detect the spontaneous emergence of life-like features, such as self-propagation and adaptability, in driven chemical systems in the laboratory. Additionally, SDAS theory may be useful for exploring general properties of other complex systems.

Mathematical Modeling of a Supramolecular Assembly for Pyrophosphate Sensing

The power of sensing molecules is often characterized in part by determining their thermodynamic/dynamic properties, in particular the binding constant of a guest to a host. In many studies, traditional nonlinear regression analysis has been used to determine the binding constants, which cannot be applied to complex systems and limits the reliability of such calculations. Supramolecular sensor systems include many interactions that make such chemical systems complicated. The challenges in creating sensing molecules can be significantly decreased through the availability of detailed mathematical models of such systems. Here, we propose uncovering accurate thermodynamic parameters of chemical reactions using better-defined mathematical modeling-fitting analysis is the key to understanding molecular assemblies and developing new bio/sensing agents. The supramolecular example we chose for this investigation is a self-assembled sensor consists of a synthesized receptor, DPA (DPA = dipicolylamine)-appended phenylboronic acid (1) in combination with Zn2+(1.Zn) that forms various assemblies with a fluorophore like alizarin red S (ARS). The self-assemblies can detect multi-phosphates like pyrophosphate (PPi) in aqueous solutions. We developed a mathematical model for the simultaneous quantitative analysis of twenty-seven intertwined interactions and reactions between the sensor (1.Zn-ARS) and the target (PPi) for the first time, relying on the Newton-Raphson algorithm. Through analyzing simulated potentiometric titration data, we describe the concurrent determination of thermodynamic parameters of the different guest-host bindings. Various values of temperatures, initial concentrations, and starting pHs were considered to predict the required measurement conditions for thermodynamic studies. Accordingly, we determined the species concentrations of different host-guest bindings in a generalized way. This way, the binding capabilities of a set of species can be quantitatively examined to systematically measure the power of the sensing system. This study shows analyzing supramolecular self-assemblies with solid mathematical models has a high potential for a better understanding of molecular interactions within complex chemical networks and developing new sensors with better sensing effects for bio-purposes.

Direct and Indirect Chemiluminescence: Reactions, Mechanisms and Challenges

Emission of light by matter can occur through a variety of mechanisms. When it results from an electronically excited state of a species produced by a chemical reaction, it is called chemiluminescence (CL). The phenomenon can take place both in natural and artificial chemical systems and it has been utilized in a variety of applications. In this review, we aim to revisit some of the latest CL applications based on direct and indirect production modes. The characteristics of the chemical reactions and the underpinning CL mechanisms are thoroughly discussed in view of studies from the very recent bibliography. Different methodologies aiming at higher CL efficiencies are summarized and presented in detail, including CL type and scaffolds used in each study. The CL role in the development of efficient therapeutic platforms is also discussed in relation to the Reactive Oxygen Species (ROS) and singlet oxygen (1O2) produced, as final products. Moreover, recent research results from our team are included regarding the behavior of commonly used photosensitizers upon chemical activation under CL conditions. The CL prospects in imaging, biomimetic organic and radical chemistry, and therapeutics are critically presented in respect to the persisting challenges and limitations of the existing strategies to date.

Novel Sand Conglomeration Treatment Prevents Sand Production and Enhances Well Productivity: Offshore Caspian Case Study

Many oil producing wells, globally, experience sand production problems when reservoir rock consists of unconsolidated sand. Several wells in the Dzheitune oil field are experiencing a similar challenge. Production of formation fines and sand has caused accumulation of fill and wellbore equipment failures and has necessitated periodical and costly coiled tubing-assisted wellbore cleanout operations. A novel chemical treatment tested in the oil field to tackle the challenge led to positive results. A well with a relatively short target perforation interval was selected as a candidate for the trial sand conglomeration treatment to avoid any uncertainties related to zone coverage. Pre-requisite sand agglomeration and chemical-crude oil compatibility laboratory studies were carried out to optimize the main system and preflush fluid formulations. Once the laboratory testing was complete, a step-rate test was performed to determine the maximum injection rate below formation fracturing pressure. The chemical systems were prepared using standard blending equipment. The preflush fluid was injected to prepare the treated zone. The main fluid was then injected into the reservoir in several cycles at matrix rate by a bullheading process. Upon completion of the treatment, the well was shut in for several days for optimal agglomeration (conglomeration) before the well was slowly put on production. A long-term increase in the productivity index and sand-free flow rate with no damage to the wellbore or the reservoir were observed. The technology demonstrated its efficiency in preventing and controlling sand production; avoiding frequent, time-consuming, costly wellbore cleanout operations; and producing hydrocarbons at reduced drawdown pressure.

An Electric Field–Based Approach for Quantifying Volumes and Radii of Chemically Affected Space

Chemical shape and size play a critical role in chemistry. The van der Waal (vdW) radii, a familiar manifold used to quantify size by assuming overlapping spheres, provides rapid estimates of size in atoms, molecules, and materials. However, the vdW method may be too rigid to describe highly polarized systems and chemical systems that stray from spherical atomistic environments. To deal with these exotic chemistries, numerous alternate methods based on electron density have been presented. While each boasts inherent generality, all define the size of a chemical system, in one way or another, by its electron density. Herein, we revisit the timeless problem of assessing sizes of atoms and molecules, instead through examination of the electric field produced by them. While conceptually different than nuclei-centered methods like that of van der Waal, the field assesses chemically affected volumes. This approac

World's First Successful Coiled Tubing Intervention to Stimulate Four Laterals in a Single Trip

Drilling a multilateral well is generally recommended for several reasons such as achieving higher productivity indices and improving recovery in tight, low-permeable zones. While the many benefits of multilateral wells are attractive, they also have drawbacks which make these wells challenging. A key challenge is how to effectively stimulate all the laterals after they have been drilled. This paper presents the application of a unique intervention technique in a multilateral well to stimulate several laterals in a single run. To increase reservoir contact area the operator drilled a multilateral well composed of 4 legs. This was carried out despite the absence of proven ways to stimulate each lateral individually. This intervention would also present the following challenges: Well displacement and stimulation would require multiple re-entries into each lateral, all conducted from a drilling rig. All the laterals were known to branch off from the low side of the bore, so individual lateral and main-bore selection would be complex. Extended reach laterals require accurate friction lockup modelling and mitigations. The unique solution presented in this paper includes the use of real-time Hybrid cable coiled tubing (RTHCT) technology. This incorporates a hybrid cable installed in the coiled tubing (CT) string and a modular sensing bottom-hole assembly (MSBHA). Electrically controlled indexing tool, inclination sensor, tool-face sensor, and hydraulic knuckle joint were used as part of the BHA to enable real-time diagnostics and dynamic controls from surface to successfully enter the lateral legs. The MSBHA enabled the orientation of the BHA electrically to any position required using software to determine and control the exact position of the BHA. This paper presents a solution to all the above-mentioned challenges. It discusses the successful implementation of the RTHCT to displace and stimulate all the 4 laterals in a single CT trip in less than seven days, pumping over 7,000 bbls of various chemical systems and covering an open-hole length of 11,176 ft. Unlike other technologies, the RTHCT technology confirmed entries into the laterals without the need to tag the bottom of the lateral, saving substantial time. Enabling re-entry in these 4 laterals represented a world record translating into major efficiency improvements and cost savings for the project. This intervention also represented the first time in Kuwait that more than 2 laterals have been accessed in a CT run.

Phase transition to chimera state in two populations of oscillators interacting via a common external environment

We consider two populations of coupled oscillators, interacting each other through a common external environment. The external environment is synthesized by the contributions from all oscillators of both populations. Such indirect coupling via an external medium arises naturally in many fields, e.g., dynamical quorum sensing in coupled biological and chemical systems. We analyze the existence and stability of a variety of stationary states on the basis of the OttAntonsen reduction method, which reveals that the interaction via an external environment gives rise to unusual collective behaviors such as the uniform drifting, non-uniform drifting and chimera states. We present a complete bifurcation diagram, which provides the underlying mechanism of the phase transition towards chimera state with the route of incoherence → uniform drift → non-uniform drift → chimera.

Independent gradient model based on Hirshfeld partition (IGMH): A new method for visual study of interactions in chemical systems

The independent gradient model (IGM) originally proposed in Phys. Chem. Chem. Phys., 19, 17928 (2017) has been increasingly popular in visual analysis of intramolecular and intermolecular interactions in recent years, and it has many clear advantages over the widely employed noncovalent interaction (NCI) method, such as intrafragment and interfragment interactions can be elegantly isolated and thus separately studied, the isosurfaces are smoother and less jaggy. However, we frequently observed that there is an evident shortcoming of IGM map in graphically studying weak interactions, that is its isosurfaces are usually too bulgy; in these cases, not only the graphical effect is poor, but also the color on some areas on the isosurfaces is inappropriate and may lead to erroneous analysis conclusions. In addition, the IGM method was originally proposed based on promolecular density, which is quite crude and does not take actual electronic structure into account. In this article, we first present a detailed overview of the IGM analysis, and then propose our new variant of IGM, namely IGM based on Hirshfeld partition of molecular density (IGMH), which replaces the free-state atomic densities involved in the IGM method with the atomic densities derived by Hirshfeld partition of actual molecular electron density. This change makes IGM have more rigorous physical background. In addition, we describe some indices defined on the top of IGM or IGMH framework to quantify contributions from various atoms or atom pairs to interaction between specific fragments. A large number of application examples in this article, including molecular and periodic systems, weak and chemical bond interactions, fully demonstrate the important value of IGMH in intuitively understanding interactions in chemical systems. Comparisons also showed that the IGMH usually has markedly better graphical effect than IGM and overcomes known problems in IGM. Currently IGMH analysis has been efficiently supported in our freely available and user-friendly wavefunction analysis code Multiwfn (http://sobereva.com/multiwfn), and a detailed tutorial is presented. We hope that IGMH will become a new popular method among chemists for exploring interactions in wide variety of chemical systems.