Theoretical Studies of a Silica Functionalized Acrylamide for Calcium Scale Inhibition.

The calcium carbonate (CaCO3) scale is one of the most common oilfield scales and oil and gas production bane. CaCO3 scale can lead to a sudden halt in production or, worst-case scenario, accidents; therefore, CaCO3 scale formation prevention is essential for the oil and gas industry. Scale inhibitors are chemicals that can mitigate this problem. We used two popular theoretical techniques in this study: Density Functional Theory (DFT) and Ab Initio Molecular Dynamics (AIMD). The objective was to investigate the inhibitory abilities of mixed oligomers, specifically acrylamide functionalized silica (AM-Silica). DFT studies indicate that Ca2+ does not bind readily to acryl acid and acrylamide; however, it has a good binding affinity with PAM and Silica functionalized PAM. The highest binding affinity occurs in the silica region and not the -CONH functional groups. AIMD calculations corroborate the DFT studies, as observed from the MD trajectory that Ca2+ binds to PAM-Silica by forming bonds with silicon; however, Ca2+ initially forms a bond with silicon in the presence of water molecules. This bonding does not last long, and it subsequently bonds with the oxygen atoms present in the water molecule. PAM-Silica is a suitable calcium scale inhibitor because of its high binding affinity with Ca2+. Theoretical studies (DFT and AIMD) have provided atomic insights on how AM-Silica could be used as an efficient scale inhibitor.

Calcite Scale Inhibition Using Environmental-Friendly Amino Acid Inhibitors: DFT Investigation.

Scale prevention is a long-term challenge. It is essential for ensuring the optimum utilization of oil and gas wells and minimizing economic losses due to disruptions in the hydrocarbon flow. Among the commonly precipitated scales is calcite, especially in oilfield production facilities. Previous studies on scale inhibitors have focused on investigating the performance of several phosphonates and carboxylates. However, the increased environmental awareness has pushed toward investigating environmental-friendly inhibitors. Research studies demonstrated the potential of using amino acids as standalone inhibitors or as inhibitor-modifying reagents. In this study, 10 amino acids for calcite inhibitors have been investigated using molecular simulations. Eco-toxicity, quantum chemical calculations, binding energy, geometrical, and charge analyses were all evaluated to gain a holistic view of the behavior and interaction of these inhibitors with the calcite {1 0 4} surface. According to the DFT simulation, alanine, aspartic acid, phenylalanine, and tyrosine amino acids have the best inhibitor features. The results revealed that the binding energies were -2.16, -1.75, -2.24, and -2.66 eV for alanine, aspartic acid, phenylalanine, and tyrosine, respectively. Therefore, this study predicted an inhibition efficiency of the order tyrosine > phenylalanine > alanine > aspartic acid. The predicted inhibition efficiency order reveals agreement with the reported experimental results. Finally, the geometrical and charge analyses illustrated that the adsorption onto calcite is physisorption in the acquired adsorption energy range.

Computational Screening of Potential Inhibitors of Desulfobacter postgatei for Pyrite Scale Prevention in Oil and Gas Wells.

Sulfate-reducing bacteria (SRB), such as Desulfobacter postgatei are found in oil wells. However, they lead to the release of hydrogen sulfide. This in turn leads to the iron sulfide scale formation (pyrite). ATP sulfurylase is an enzyme present in SRB, which catalyzes the formation of adenylyl sulfate (APS) and inorganic pyrophosphatase (PPi) from ATP and sulfate. This reaction is the first among many in hydrogen sulfide production by D. postgatei . Consensus scoring using molecular docking and machine learning was used to identify three potential inhibitors of ATP sulfurylase from a database of about 40 million compounds. These selected hits ((S,E)-1-(4-methoxyphenyl)-3-(9-((m-tolylimino)methyl)-9,10-dihydroanthracen-9-yl)pyrrolidine-2,5-dione; methyl 2-[[(1S)-5-cyano-2-imino-1-(4-phenylthiazol-2-yl)-3-azaspiro[5.5]undec-4-en-4-yl]sulfanyl]acetate; and (4S)-4-(3-chloro-4-hydroxy-phenyl)-1-(6-hydroxypyridazin-3-yl)-3-methyl-4,5-dihydropyrazolo[3,4-b]pyridin-6-ol), known as A, B, and C, respectively) all had good binding affinities with ATP sulfurylase and were further analyzed for their toxicological properties. Compound A had the highest docking score. However, based on the physicochemical and toxicological properties, only compound C was predicted to be both safe and effective as a potential inhibitor of ATP sulfurylase, hence the preferred choice. The molecular interactions of compound C revealed favorable interactions with the following residues: LEU213, ASP308, ARG307, TRP347, LEU224, GLN212, MET211, and HIS309.

Electrochemical removal of pyrite scale using green formulations.

Pyrite scale formation is a critical problem in the hydrocarbon production industry; it affects the flow of hydrocarbon within the reservoir and the surface facilities. Treatments with inorganic acids, such as HCl, results in generation toxic hydrogen sulfide, high corrosion rates, and low dissolving power. In this work, the dissolution of pyrite scale is enhanced by the introduction of electrical current to aid the chemical dissolution. The electrolytes used in this study are chemical formulations mainly composed of diethylenetriamine-pentaacetic acid-potassium (DTPAK5) with potassium carbonate; diethylenetriamine pentaacetic acid sodium-based (DTPANa5), and L-glutamic acid-N, N-diacetic acid (GLDA). DTPA and GLDA have shown some ability to dissolve iron sulfide without generating hydrogen sulfide. The effect of these chemical formulations, disc rotational rate and current density on the electro-assisted dissolution of pyrite are investigated using Galvanostatic experiments at room temperature. The total iron dissolved of pyrite using the electrochemical process is more than 400 times higher than the chemical dissolution using the same chelating agent-based formulation and under the same conditions. The dissolution rate increased by 12-folds with the increase of current density from 5 to 50 mA/cm2. Acid and neutral formulations had better dissolution capacities than basic ones. In addition, doubling the rotational rate did not yield a significant increase in electro-assisted pyrite scale dissolution. XPS analysis confirmed the electrochemical dissolution is mainly due to oxidation of Fe2+ on pyrite surface lattice to Fe3+. The results obtained in this study suggest that electro-assisted dissolution is a promising technique for scale removal.

Dissolution Kinetics of Different Inorganic Oilfield Scales in Green Formulations.

Scale mineral deposition is a critical problem that hinders the daily production of oil and gas fields. Chemical removal of these scales, based on the scale type, is common. In this paper, borax and diethylene tremaine penta acetic (DTPA) acid-based formulations are used for the removal of sulfides, carbonates, and sulfate scales. In particular, the dissolution rates of sulfide (pyrite, pyrrhotite, and galena), sulfate (celestite and barite), and carbonate (calcite) scales were investigated in a rotating disc apparatus at typical well conditions. Scanning electron microscopy-energy-dispersive X-ray and X-ray diffraction analyses were performed for characterizing scale composition and type. The effect of temperature, scale type, and formulation on the dissolution rate is studied. Even though borax formulation has been developed for the sulfide scale removal, it showed a high dissolution rate for the carbonate scale (7.23 × 10-7 mol·L-1·s-1·cm-2). For the sulfide scale, the highest dissolution in borax formulation was obtained with galena (lead sulfide, PbS), followed by pyrrhotite, and the lowest dissolution was reported for pyrite (1.55 × 10-8 mol·L-1·s-1·cm-2). Borax formulation was found to be inefficient in the removal of sulfate scales with a dissolution rate lower than carbonate and sulfide scales by 3 and 2 orders of magnitude, respectively. Similarly, DTPA-based formulation has yielded the highest dissolution for the carbonate scale (7.98 × 10-6 mol·L-1·s-1·cm-2). However, for sulfate, DTPA-based formulation showed better performance than borax. The increase in temperature leads to an increase in the dissolution rate for almost all types of scales; however, DTPA-based formulation showed improved performance with temperature. Both formulations are efficient in removing sulfate- and sulfide-rich scales. The experimental results of DTPA have been validated by density functional theory calculations of binding energies between DTPA and metal ions present in the mixed scale.

Development of a New Borax-Based Formulation for the Removal of Pyrite Scales.

In the oil and gas industry, pyrite forms one of the most hardened scales in reservoirs, which hinders the flow of fluids. Consequently, this leads to blockage of the downhole tubular, formation damage, and complete shutdown of production and operational processes. Herein, a new green formulation based on borax (K2B4O7) is proposed for pyrite scale removal. The temperature effect, disk rotational speed, and borax concentration have been investigated using a rotating disk apparatus. Also, XPS and SEM-EDX analyses were conducted on the pyrite disk surface before and after the treatment with the green formulation. The new formulation showed the potential ability to dissolve pyrite without generating the toxic hydrogen sulfide (H2S). The dissolution rate of the scale in the new formulation is increased by 16% compared to that in a previous green formulation composed of 20 wt %DTPA+9 wt % K2CO3. Molecular modeling technique using DFT was used to study the solvation energies of Fe2+ and Fe3+. The latter had a higher solvation energy than the former, which confirmed that upon using the borax-based formulation to oxidize Fe2+ to Fe3+. It will aid the dissolution of pyrite scales. The new formulation achieved a corrosion rate that is 25 times lower than that of 15 wt % HCl, which is commercially used in treating scales. Finally, the proposed new formulation does not require the use of corrosion inhibitors; hence, it is expected to result in a more economical scale treatment method.

COVID-19: CADD to the rescue.

The recent outbreak of the deadly COVID-19 disease, being caused by the novel coronavirus (SARS-CoV-2), has put the world on red alert as it keeps spreading and recording more fatalities. Research efforts are being carried out to curtail the disease from spreading as it has been declared as of global health emergency. Hence, there is an exigent need to identify and design drugs that are capable of curing the infection and hinder its continual spread across the globe. Herein, a computer-aided drug design tool known as the virtual screening method was used to screen a database of 44 million compounds to find compounds that have the potential to inhibit the surface glycoprotein responsible for virus entry and binding. The consensus scoring approach selected three compounds with promising physicochemical properties and favorable molecular interactions with the target protein. These selected compounds can undergo lead optimization to be further developed as drugs that can be used in treating the COVID-19 disease.

Effect of surface morphology on methane interaction with calcite: a DFT study.

Natural gas, consisting primarily of methane, is found in carbonate reservoirs of which calcite is major component. However, the complexity and heterogeneity of carbonate reservoirs remain a major challenge in estimating ultimate recovery. Herein, density functional theory calculations are employed to study the effect of surface morphology on the adsorption of CH4 on the surface of CaCO3 (calcite). Among the 9 different surface symmetries considered, the strongest adsorption (and consequently the largest adsorption capacity) of methane is found for the 110 surface of the material. In fact, the adsorption capacity of this surface is more than an order of magnitude larger than the one for the 104 surface, which is the lowest energy surface for the calcite. The obtained results are explained by structural analysis and charge calculations. These findings can be useful for the estimation of the ultimate gas recovery taking into account heterogeneous porosity and permeability of the carbonate reservoirs.

Density-Functional Theory Investigation of Barite Scale Inhibition Using Phosphonate and Carboxyl-Based Inhibitors.

Scale deposition is a critical issue in oil and gas exploration and production processes, causing significant blocking in tubing and consequently flow assurance and economic losses. Most studies addressing the scale formation have been limited on the experimental impact of different variables on scale formation. In this work, the inhibition of barite scale deposition was investigated by employing molecular simulations for three different scale inhibitors, namely, polyaspartic acid (PASP), nitrilotrimethylenephosphonate (NTMP), and dimethylenetriaminepenta(methylene-phosphonic acid) (DETPMP). Geometrical analyses were used to explore the performances of the inhibitors and visualize the outcomes. quantitative structure activity relationship parameters were also used to predict the activity of the inhibitors in the system. The order of the inhibitors is in agreement with the experiments with the following values for binding energies: -1.06, -0.17, and -2.33 eV for PASP, NTMP, and DETPMP, respectively. The results of this study indicated that the inhibition strength of the three inhibitors on barite scale formation can be sequenced as DETPMP > PASP > NTMP. Moreover, the ecological toxicity (eco-tox) properties were predicted, and the environmental impact of the different inhibitors was assessed. All inhibitors showed comparable eco-tox properties and predicted to be soluble in water. Molecular simulations proved to be an effective tool in the prediction of the performance and toxicity of barite scale inhibitors.

Synthesis, spectroscopic characterization, molecular docking and theoretical studies (DFT) of N-(4-aminophenylsulfonyl)-2-(4-isobutylphenyl) propanamide having potential enzyme inhibition applications.

A mutual prodrug (1) of ibuprofen and sulphanilamide has been synthesized with dual activity and improved toxicity profile. The synthesized compound has been characterized by elemental analysis, FT-IR, 1HNMR, 13CNMR and ESI-MS. The molecular geometry of the compound (1) was optimized using density functional theory (DFT/B3LYP) method with the 6-311G(d,p) basis sets in ground state. Geometric parameters (bond lengths, bond angles, torsion angles), vibrational assignments, chemical shifts and thermodynamics of the compound (1) has been calculated theoretically and compared with the experimental data. Comparative AutoDock study of compound (1) with cyclooxygenase enzymes (COX-1 and COX-2) were performed involving docking for possible selectivity of our prodrug within the two Cox enzymes. The highest binding affinities of -8.7 Kcal/mol and -8.1 Kcal/mol has been obtained for COX-1 and COX-2 enzymes respectively. Compound (1) exhibited enhanced anti-inflammatory, anti-ulcer and free radical scavenging activities as compared with the parent drugs. Based on various in vitro and in vivo tests it is suggested that the Compound (1) is more active than the parent drugs. Moreover, LD50 of compound (1) is higher than parent drug i.e. ibuprofen and sulphanilamide suggesting that the synthesized compound is much safer than its parent analogous.

Molecular dynamics and combined docking studies for the identification of Zaire ebola virus inhibitors.

Ebola virus (EBOV) is a lethal human pathogen with a risk of global spread of its zoonotic infections, and Ebolavirus Zaire specifically has the highest fatality rate amongst other species. There is a need for continuous effort towards having therapies, as a single licensed treatment to neutralize the EBOV is yet to come into reality. This present study virtually screened the MCULE database containing almost 36 million compounds against the structure of a Zaire Ebola viral protein (VP) 35 and a consensus scoring of both MCULE and CLCDDW docking programs remarked five compounds as potential hits. These compounds, with binding energies ranging from -7.9 to -8.9 kcal/mol, were assessed for predictions of their physicochemical and bioactivity properties, as well as absorption, distribution, metabolism, excretion, and toxicity (ADMET) criteria. The results of the 50 ns molecular dynamics simulations showed the presence of dynamic stability between ligand and protein complexes, and the structures remained significantly unchanged at the ligand-binding site throughout the simulation period. Both docking analysis and molecular dynamics simulation studies suggested strong binding affinity towards the receptor cavity and these selected compounds as potential inhibitors against the Zaire Ebola VP 35. With respect to inhibition constant values, bioavailability radar and other physicochemical properties, compound A (MCULE-1018045960-0-1) appeared to be the most promising hit compound. However, the ligand efficiency and ligand efficiency scale need improvement during optimization, and also validation via in vitro and in vivo studies are necessary to finally make a lead compound in treating Ebola virus diseases. Communicated by Ramaswamy H. Sarma.

Molecular Modeling Study toward Development of H2S-Free Removal of Iron Sulfide Scale from Oil and Gas Wells.

A common problem that faces the oil and gas industry is the formation of iron sulfide scale in various stages of production. Recently an effective chemical formulation was proposed to remove all types of iron sulfide scales (including pyrite), consisting of a chelating agent diethylenetriaminepentaacetic acid (DTPA) at high pH using potassium carbonate (K2CO3). The aim of this molecular modeling study is to develop insight into the thermodynamics and kinetics of the chemical reactions during scale removal. A cluster approach was chosen to mimic the overall system. Standard density functional theory (B3LYP/6-31G*) was used for all calculations. Low spin K4Fe(II)4(S2H)12 and K3Fe(II)(S2H)5 clusters were derived from the crystal structure of pyrite and used as mimics for surface scale FeS2. In addition, K5DTPA was used as a starting material too. High spin K3Fe(II)DTPA, and K2S2 were considered as products. A series of K m Fe(II)(S2H) n complexes (m = n-2, n = 5-0) with various carboxylate and glycinate ligands was used to establish the most plausible reaction pathway. Some ligand exchange reactions were investigated on even simpler Fe(II) complexes in various spin states. It was found that the dissolution of iron sulfide scale with DTPA under basic conditions is thermodynamically favored and not limited by ligand exchange kinetics as the activation barriers for these reactions are very low. Singlet-quintet spin crossover and aqueous solvation of the products almost equally contribute to the overall reaction energy. Furthermore, seven-coordination to Fe(II) was observed in both high spin K3Fe(II)DTPA and K2Fe(II)(EDTA)(H2O) albeit in a slightly different manner.

Silver-loaded graphene as an effective SERS substrate for clotrimazole detection: DFT and spectroscopic studies.

Vibrational infrared, Raman and surface-enhanced Raman scattering (SERS) spectra of clotrimazole (CTZ) were documented and evaluated. Density-functional theory, B3LYP/6-311++G(d,p), approach was implemented to identify the possible conformations, develop the electrostatic potential map, evaluate frontier molecular orbitals and calculate the vibrational spectra of the target compound. The silver-loaded graphene was shown to be an effective SERS substrate for CTZ trace detection. The SERS spectrum showed two enhanced bands at 670 cm-1 and 700 cm-1 which confirmed the absorption of the silver substrate through chlorine and nitrogen atoms. A detection limit as low as 5 nM could be reached with a determination coefficient of 0.9988 using the band at 670 cm-1. The protein-ligand interaction with Secreted Aspartic Proteinase 2 (SAP2) of C. albicans showed that the four stable forms of CTZ maintain a free energy of binding of 6-7 kcal/mol, which could give insights into the mode of action in treating Candidiasis.

Structure based virtual screening of the Ebola virus trimeric glycoprotein using consensus scoring.

Ebola virus (EBOV) causes zoonotic viral infection with a potential risk of global spread and a highly fatal effect on humans. Till date, no drug has gotten market approval for the treatment of Ebola virus disease (EVD), and this perhaps allows the use of both experimental and computational approaches in the antiviral drug discovery process. The main target of potential vaccines that are recently undergoing clinical trials is trimeric glycoprotein (GP) of the EBOV and its exact crystal structure was used in this structure based virtual screening study, with the aid of consensus scoring to select three possible hit compounds from about 36 million compounds in MCULE's database. Amongst these three compounds, (5R)-5-[[5-(4-chlorophenyl)-1,2,4-oxadiazol-3-yl]methyl]-N-[(4-methoxyphenyl)methyl]-4,5-dihydroisoxazole-3-carboxamide (SC-2, C21H19ClN4O4) showed good features with respect to drug likeness, ligand efficiency metrics, solubility, absorption and distribution properties and non-carcinogenicity to emerge as the most promising compound that can be optimized to lead compound against the GP EBOV. The binding mode showed that SC-2 is well embedded within the trimeric chains of the GP EBOV with molecular interactions with some amino acids. The SC-2 hit compound, upon its optimization to lead, might be a good potential candidate with efficacy against the EBOV pathogen and subsequently receive necessary approval to be used as antiviral drug for the treatment of EVD.

Spherical silver nanoparticles as substrates in surface-enhanced Raman spectroscopy for enhanced characterization of ketoconazole.

A new method was developed for the characterization and detection of ketoconazole using surface enhanced Raman spectroscopy (SERS) by designing substrates and performing the bands' assignments. Thus, spherical silver nanoparticles (Ag-NPs) were synthesized by a reduction method and designed as substrates for SERS application. The Ag-NPs were characterized using a scanning electron microscope, Fourier transformed infrared spectroscopy and a high-resolution transmission electron microscope. TEM results indicated that the average size of the Ag-NPs was 15nm. The UV spectrum showed a maximum absorbance of Ag-NPs at about 400nm. When Ag-NPs were used as substrates in SERS, the Raman spectra of KCZ showed a significant enhancement of the Raman bands. An important finding is a linear relationship between the logarithmical scale of KCZ concentration and the intensity of the SERS bands, for example at 1050cm-1 of KCZ, which is due to the CN vibration. This was optimized and utilized to develop a calibration curve, which was then used for the detection of the KCZ in real pharmaceutical samples. The method has the advantages of a wide dynamic range with a high coefficient of determination and detection limit calculated based on the signal-to-noise ratio of 3, was 2.6×10-10M and the limit of quantification was 7.8×10-10M. The potential applications that take advantage of the high SERS sensitivity of this method are discussed for practical KCZ analysis where were quantified with this method.

Identification of potential inhibitors against the Zika virus using consensus scoring.

The Zika virus (ZIKV) is a life threatening pathogen of zoonotic importance with prevalence in some parts of Africa and America. Unfortunately, there is yet to be a single approved vaccine or antiviral drug to treat the diseases and deformations being caused by the Zika virus infection. In this study, about 36 million compounds from MCULE database were virtually screened against a real matured ZIKV protein using a consensus scoring method to get improved hit rates. The consensus scoring method combined the result from the 25 top ranked molecules from both MCULE and Drug Score eXtended (DSX) docking programs which led to the selection of two hit compounds. The inhibition constant (Ki) values of 0.08 and 0.30µm were obtained for the two selected compounds MCULE-8830369631-0-1 and MCULE-9236850811-0-1 respectively, to remark them as hit compounds. The molecular interactions of the two selected hit compounds with the amino acids (ALA 48, ILE 49, ILE 468 and LEU 472) present in the ZIKV protein indicated that they both have similar binding modes. The result of the computationally predicted physicochemical properties including ADMET for the selected compounds showed their great potential in becoming lead compounds upon optimization and thus could be used in treating the Zika virus diseases.