Computational Chemistry Tools Research Articles

A Review on Molecular Docking on HDAC Isoforms: Novel Tool for Designing Selective Inhibitors.

Research into histone deacetylases (HDACs) has experienced a remarkable surge in recent years. These enzymes are key regulators of several fundamental biological processes, often associated with severe and potentially fatal diseases. Inhibition of their activity represents a promising therapeutic approach and a prospective strategy for the development of new therapeutic agents. A critical aspect of their inhibition is to achieve selectivity in terms of enzyme isoforms, which is essential to improve treatment efficacy while reducing undesirable pleiotropic effects. The development of computational chemistry tools, particularly molecular docking, is greatly enhancing the precision of designing molecules with inherent potential for specific activity. Therefore, it was considered necessary to review the molecular docking studies conducted on the major isozymes of the enzyme in order to identify the specific interactions associated with each selective HDAC inhibitor. In particular, the most critical isozymes of HDAC (1, 2, 3, 6, and 8) have been thoroughly investigated within the scope of this review.

Comparison of Density-Functional Theory Dispersion Corrections for the DES15K Database.

While density-functional theory (DFT) remains one of the most widely used tools in computational chemistry, most functionals fail to properly account for the effects of London dispersion. Hence, there are many popular post-self-consistent methods to add a dispersion correction to the DFT energy. Until now, the most popular methods have never been compared on equal footing due to not being implemented in the same electronic structure packages. In this work, we performed a large-scale benchmarking study, directly comparing the accuracy of the exchange-hole dipole moment (XDM), D3BJ, D4, TS, MBD, and MBD-NL dispersion models when applied to the recent DES15K database of nearly 15,000 molecular complexes at both expanded and compressed geometries. Our study showed similarly good performance for all dispersion methods (except TS) when applied to neutral complexes. However, they all performed worse for ionic complexes, particularly those involving dications of alkaline earth metals, due to systematic overbinding by the base PBE0 density functional. Investigation of the largest outliers also revealed that only the MBD and MBD-NL methods demonstrate surprising errors for complexes involving alkali metal cations at compressed geometries where they tended to significantly overbind. As we would expect minimal dispersion binding for such complexes, we further investigated the origins of these errors for the potential energy curve of a model cation-π complex. Overall, there is little choice between the XDM, D3BJ, D4, MBD, and MBD-NL dispersion methods for most systems. However, the MBD-based methods are not recommended for complexes involving organic species and alkali or alkaline earth metal cations, for example when modeling Li+ intercalation into graphite.

Machine learning meets quantum mechanics in catalysis

Over the past decade many researchers have applied machine learning algorithms with computational chemistry and materials science tools to explore properties of catalysts. There is a rapid increase in publications demonstrating the use of machine learning for rational catalyst design. In our perspective, targeted tools for rational catalyst design will continue to make significant contributions. However, the community should focus on developing high-throughput simulation tools that utilize molecular dynamics capabilities for thorough exploration of the complex potential energy surfaces that exist, particularly in heterogeneous catalysis. Catalyst-specific databases should be developed to contain enough data to represent the complex multi-dimensional space that defines structure-function relationships. Machine learning tools will continue to impact rational catalyst design; however, we believe that more sophisticated pattern recognition algorithms would yield better understanding of structure-function relationships for heterogeneous catalysis.

Theoretical analysis of OLED performances of some aromatic nitrogen-containing ligands.

It is well-known that tris(8-hydroxyquinoline) aluminum (Alq3) complex and N,N'diphenyl-N,N'-bis(3-methylphenyl)-1,1'-diphenyl-4,4'-diamine compound (TPD) are widely used as electron transfer material (ETL) and hole transfer material (HTL) in organic light emitting diode (OLED) structure, respectively. Considering the reference materials, in the present work, the OLED performances of some cyclic aromatic structures such as 4,4'azopyridine [AZPY], 4,4'-bipyridine [BIPY], 1,2-bis[4'-(4-methylphenyl)2,2':6'2″-terpyridin6-yl]ethyne (BISTERPY), 5,5'-diamino-2,2'-bipyridine (DABP), dipyrido[3,2-a:2',3'c]phenazine (DPP), 4,7-phenanthroline (PHEN) including nitrogen atom have been theoretically analyzed. It is important to note that B3LYP/6-31G(d) and B3LYP/TZP levels of the theory were taken into account for the calculations about monomeric and dimeric structures, respectively. Additionally, the calculations of the mentioned monomeric form were performed at B3LYP-D3/6-31G, CAM-B3LYP/6-31G and ωB97X-D/6-31G(d) levels. For a detailed theoretical analysis, the reorganization energies (λe and λh), adiabatic and vertical ionization potentials and electron affinities, the effective transfer integrals (Ve and Vh), and the charge transfer rates (We and Wh) of all compounds were computed by means of computational chemistry tools. In the light of calculated parameters, it is determined that these mentioned aromatic cyclic structures will be used in which layers of OLED structure. The results obtained in this study will be helpful in the design and applications of new molecules as OLED materials in the future.

Organic light‐emitting diode behaviors of some synthesized platinum(II)‐based complexes

AbstractOrganic light‐emitting light diodes (OLEDs) have been increasingly used in displays, replacing liquid‐crystal displays (LCD) and light‐emitting diodes (LEDs) panels. The increase in commercial use of OLED has led to the search for OLED with high performance. For that reason, the OLED properties of monomers and dimers of some synthesized platinum(II)‐based complexes were estimated by using different computational chemistry tools with different codes. The electron/hole reorganization energies, the adiabatic/vertical ionization potentials, the adiabatic/vertical electron affinities, the chemical hardness values, the dipole moments, the frontier orbital shapes/energy levels, the energy gaps, the emission wavelengths, spin‐orbit matrix elements, the rates of reverse intersystem crossing and intersystem crossing of the investigated complexes were determined. From the theoretically obtained data, it was found that Pt(hppz)2 and Pt(fppz)2 complexes can be used as electron transfer material. Furthermore, it was stated that Pt(f2bipz)(bpy) is both electron‐blocking layer and hole blocking layer materials. Moreover, it was noted that that PtOEP complex can be utilized as a good electron injection layer and hole injection layer material. Addition to these, it was emphasized that that Pt(f2bipz)(bpy) can be considered as a good candidate for near infrared organic light emitting diodes and thermal activated delayed fluorescent organic light emitting diodes. In light of computational chemistry, it should be expected that the study will provide a great contribution to studies related to organic light emitting diodes.

Chemical Reactivities and Organic Light-emitting Diode Properties of some Polyaromatic Molecules

High-performance organic-light emitting diode (OLED) display panels have been very popular lately due to their many advantages compared to liquid-crystal display (LCD) and light-emitting diode (LED) panels. It is also well known that the materials used in OLED panels are important in determining OLED performance. Starting with the selection of materials which have rich π-electrons will be a good start for the design of high-performance OLED materials. For this aim, the OLED properties of some cyclic aromatic structures with rich π-electrons such as 2,2ꞌ-bi-1,6-naphthyridine (BNP), 1,6-bis(4ꞌ-pyridine)-2,5-diazahexane (BPDH), 3,3ꞌ-bis[3-(2-pyridyl)pyrazol-1-yl]biphenyl (BPPB), 5,5ꞌ-dicyano-2,2ꞌ-bipyridine (DCBP), 2,2ꞌ-dimethyl-4,4ꞌ-bipyrimidine (DMBP), and 4ꞌ-phenyl-2,2ꞌ:6ꞌ2ꞌꞌterpyridine (Ph-TERPY) were theoretically analyzed using computational chemistry tools. The calculations of monomeric and dimeric structures of mentioned molecules were carried out at B3LYP/6-31G(d) and B3LYP/TZP levels, respectively. The OLED properties of the investigated compound were explained by means of OLED parameters such as the reorganization energies, adiabatic-vertical ionization potentials and adiabatic-vertical electron affinities, the effective transfer integrals, and the charge transfer ratios. In the light of computational chemistry, it is indicated that these studied molecules will be utilized in which layers of OLED device. In addition to OLED analysis, in the light of the calculated reactivity descriptors, the chemical reactivities of the studied molecules were discussed.

Interaction mechanism of triclosan on pristine microplastics

Urban wastewaters comprise different hydrophobic pollutants such as microplastics (MPs), pharmaceuticals, and personal care products. Among these pollutants, triclosan (TCS) shows a worrying interaction ability with MPs; recent studies show MPs serve as a vector between TCS and aquatic environments, whose interaction is still being studied to understand their combined toxicity and transport ability. Using computational chemistry tools, this work evaluates the TCS-MPs interaction mechanism, including pristine polymers, i.e., aliphatic polyamides (PA), polyethylene (PE), polystyrene (PS), polyvinyl chloride (PVC), and polyethylene terephthalate (PET). Our results show that TCS adsorption on MPs solely occurs via physisorption, where PA reaches the higher adsorption ability. Remarkably, MPs reach higher or comparable adsorption stability than carbon-based materials, boron nitrides, and minerals, indicating their worrying transport properties. Also, the adsorption capacity is strongly influenced by entropy changes rather than thermal effects, which determine the different sorption capacities among polymers and agree well with reported sorption capacities from adsorption kinetic experiments in the literature. MPs show a polar and highly susceptible surface to establish electrostatics and dispersion effects on TCS. Accordingly, the TCS-MPs interaction mechanism arises from the interplay between electrostatics and dispersion forces, with a combined contribution of 81–93 %. Specifically, PA and PET maximize the electrostatic effects, while PE, PP, PVC, and PS maximize the dispersion effects. From the chemical viewpoint, TCS-MPs complexes interact by a series of pairwise interactions such as Van der Waals, hydrogen bonding, C-H⋯π, C-H⋯C-H, C-Cl⋯C-H, and C-Cl⋯Cl-C. Finally, the mechanistic information explains the effects of temperature, pressure, aging, pH, and salinity on TCS adsorption. This study quantitatively elucidates the interaction mechanism of TCS-MP systems, which were hard to quantify to date, and explains the TCS-MPs sorption performance for sorption/kinetic studies.

Simulations of Amyloid-Forming Peptides in the Crystal State

There still is little treatment available for amyloid diseases, despite their significant impact on individuals and the social and economic implications for society. One reason for this is that the physical nature of amyloid formation is not understood sufficiently well. Therefore, fundamental research at the molecular level remains necessary to support the development of therapeutics. A few structures of short peptides from amyloid-forming proteins have been determined. These can in principle be used as scaffolds for designing aggregation inhibitors. Attempts to this end have often used the tools of computational chemistry, in particular molecular simulation. However, few simulation studies of these peptides in the crystal state have been presented so far. Hence, to validate the capability of common force fields (AMBER19SB, CHARMM36m, and OPLS-AA/M) to yield insight into the dynamics and structural stability of amyloid peptide aggregates, we have performed molecular dynamics simulations of twelve different peptide crystals at two different temperatures. From the simulations, we evaluate the hydrogen bonding patterns, the isotropic B-factors, the change in energy, the Ramachandran plots, and the unit cell parameters and compare the results with the crystal structures. Most crystals are stable in the simulations but for all force fields there is at least one that deviates from the experimental crystal, suggesting more work is needed on these models.

Theoretical FRET Efficiency of an Antenna Material Containing Natural Dyes and Zeolite L.

We calculated the Förster resonance energy-transfer (FRET) efficiency of a theoretical host-guest composite formed by all-trans β-cryptoxanthin (BCRY), all-trans zeaxanthin (ZEA), and a zeolite-LTL (Linde Type L) nanochannel with the help of computational chemistry tools. Climate change demands urgently the development of novel renewable energies, and in such a context, artificial photosynthesis arises as a promising technology capable of contributing to satisfying humankind's energy needs. All artificial photosynthetic devices need antennas to harvest and transfer energy to a reaction center efficiently. Antenna materials integrated by highly fluorescent synthetic pigments embedded onto the nanochannels of a zeolite-LTL have already been shown experimentally to be very efficient supramolecular assemblies. However, research work computing the efficiency of an antenna made of nonfluorescent natural pigments and a zeolite-LTL nanochannel has not been undertaken yet, at least to our knowledge. Fortunately, natural dyes possess outstanding features to study them dynamically; they are environmentally friendly, inexpensive, ubiquitous, and abundant. Density functional theory (DFT) methods were chiefly employed along with the CAM-B3LYP functional and the 3-21G*/6-311+G(d,p) basis sets. The ONIOM method enabled geometry and energy calculations of dyes inside the zeolite-LTL (ZL) nanochannel. The Förster resonance energy-transfer (FRET) efficiency and the Förster radius of the composite were 40.9% and 24.9 Å, respectively. Theoretical findings suggested that this composite might contribute to diminishing costs and improving the environmental friendliness of an antenna system.

Cu+/Ag+ Competition in Type I Copper Proteins (T1Cu).

Due to the similarity in the basic coordination behavior of their mono-charged cations, silver biochemistry is known to be linked to that of copper in biological systems. Still, Cu+/2+ is an essential micronutrient in many organisms, while no known biological process requires silver. In human cells, copper regulation and trafficking is strictly controlled by complex systems including many cytosolic copper chaperones, whereas some bacteria exploit the so-called "blue copper" proteins. Therefore, evaluating the controlling factors of the competition between these two metal cations is of enormous interest. By employing the tools of computational chemistry, we aim to delineate the extent to which Ag+ might be able to compete with the endogenous copper in its Type I (T1Cu) proteins, and where and if, alternatively, it is handled uniquely. The effect of the surrounding media (dielectric constant) and the type, number, and composition of amino acid residues are taken into account when modelling the reactions in the present study. The obtained results clearly indicate the susceptibility of the T1Cu proteins to a silver attack due to the favorable composition and geometry of the metal-binding centers, along with the similarity between the Ag+/Cu+-containing structures. Furthermore, by exploring intriguing questions of both metals' coordination chemistry, an important background for understanding the metabolism and biotransformation of silver in organisms is provided.

Exploration of bioactive compounds from Mangifera indica (Mango) as probable inhibitors of thymidylate synthase and nuclear factor kappa-B (NF-Κb) in colorectal cancer management

Abstract This research is aimed at investigating the anti-colorectal cancer activities of phytochemicals from Mangifera indica (Mango) via the inhibition of thymidylate synthase (TS) and Nuclear Factor kappa B (NF–κB) using computational chemistry tools. Ligands (141 phytochemicals previously isolated from mangoes) and reference drugs (Raltitrexed and Emetine), the drug inhibitors of TS and NF–κB, respectively) were subjected to screening via ADMET profiling, drug-likeness analysis, oral bioavailability, PASS profile, and molecular interactions. Ligands that passed the previously mentioned screening were docked in duplicate against the target receptors (TS and NF–κB) using PyRx software. The mean values were calculated to obtain suitable docking scores. The analysis showed that TS was strongly inhibited by Friedelan-3beta-Ol with its lower binding energy of −9.0 kcal/mol more than Raltitrexed with a binding energy of −8.7 kcal/mol. NF–κB was also inhibited by Friedelan-3beta-Ol and Friedelin with binding energies of −8.0 and −8.1 kcal/mol, respectively, more than Emetine with a binding energy of −6.4 kcal/mol. These two phytochemicals performed much better than the standard drugs, thus selected as the best hits compounds because of their ADMET profile, drug-likeness properties, bioactivity, oral bioavailability, PASS prediction, binding affinities, and their interactions with the amino acids in the active sites of the receptors. Therefore, further studies are necessary for the validation of these claims toward the development of new effective and safer anti-colorectal cancer drugs.

Computer-Aided Drug Design Project for Introductory High School Students

The pharmaceutical industry has been a major player in improving life expectancies and driving chemistry employment. While computational chemistry tools increasingly guide pharmaceutical research decisions, high school and undergraduate chemistry curricula do not reflect the prevalence of such techniques. Incorporation of computational tools into chemistry education is warranted to support industry-relevant learning experiences, student motivation to pursue chemistry careers, and public understanding of STEM careers and medicines. Therefore, this paper outlines how a computer-aided drug design (CADD) tool was introduced to high school students as a classroom project in tandem with traditional course material. Materials are provided to assist instructors in replicating this project in their own courses.

Tautomeric Equilibrium in 1-Benzamidoisoquinoline Derivatives.

In this study, the tautomeric equilibrium of a sequence of 1-benzamidoisoquinoline derivatives was investigated with the tools of NMR spectroscopy and computational chemistry. The equilibrium between different tautomers in these systems could be controlled via the substitution effect, and the relative content of the amide form varied from 74% for the strong electron-donating NMe2 substituent to 38% for the strong electron-accepting NO2 group in the phenyl ring. In contrast to the previously investigated 2-phenacylquinoline derivatives, the most stable and thus most abundant tautomer in the 1-benzamidoisoquinoline series except the two most electron-accepting substituents was an amide. The intramolecular hydrogen bond present in the enol tautomer competed with the intermolecular hydrogen bonds created with the solvent molecules and thus was not a sufficient factor to favor this tautomer in the mixture. Although routinely computational studies of tautomeric equilibrium are performed within the continuum solvent models, it is proven here that the inclusion of the explicit solvent is mandatory in order to reproduce the experimental tendencies observed for this type of system, facilitating strong intermolecular hydrogen bonds.

Hepatoprotective Activity of Lignin-Derived Polyphenols Dereplicated Using High-Resolution Mass Spectrometry, In Vivo Experiments, and Deep Learning.

Chronic liver diseases affect more than 1 billion people worldwide and represent one of the main public health issues. Nonalcoholic fatty liver disease (NAFLD) accounts for the majority of mortal cases, while there is no currently approved therapeutics for its treatment. One of the prospective approaches to NAFLD therapy is to use a mixture of natural compounds. They showed effectiveness in alleviating NAFLD-related conditions including steatosis, fibrosis, etc. However, understanding the mechanism of action of such mixtures is important for their rational application. In this work, we propose a new dereplication workflow for deciphering the mechanism of action of the lignin-derived natural compound mixture. The workflow combines the analysis of molecular components with high-resolution mass spectrometry, selective chemical tagging and deuterium labeling, liver tissue penetration examination, assessment of biological activity in vitro, and computational chemistry tools used to generate putative structural candidates. Molecular docking was used to propose the potential mechanism of action of these structures, which was assessed by a proteomic experiment.

The interaction mechanism of polystyrene microplastics with pharmaceuticals and personal care products

Microplastics (MPs) have been detected in the hydrosphere, with hazardous implications in transporting coexisting water pollutants. Our knowledge about the interaction mechanisms that MPs establish with organic pollutants are still growing, which is essential to understand the adsorption properties of MPs and their relative stability with adsorbates. Here, we used classical (force field methods) and ab-initio (density functional theory) computational chemistry tools to characterize the interaction mechanisms between Polystyrene-MPs (PS-MPs) and pharmaceuticals/personal care products (PPCPs). Adsorption conformations and energies, thermochemistry, binding, and energy decomposition analyses were performed to obtain the quantitative mechanistic information. Our results show that PS-MPs have permanent dipoles, increasing the interaction with neutral PPCPs while repelling the charged pollutants; in all cases, a stable physisorption takes place. Moreover, PS-MPs increase their solubility upon pollutant adsorption due to an increase in the dipole moment, increasing their co-transport ability in aqueous environments. The stability of the PS-MPs/PPCPs complexes is further confirmed by thermochemical and molecular dynamics trajectory analysis as a function of temperature and pressure. The interaction mechanism of high pKa pollutants (pKa > 5) is due to a balanced contribution of electrostatic and dispersion forces, while the adsorption of low pKa pollutants (pKa < 5) maximizes the electrostatic forces, and steric repulsion effects explain their relative lower adsorption stability. In this regard, several pairwise intermolecular interactions are recognized as a source of stabilization in the PS-MPs/PPCPs binding: hydrogen bonding, π-π, OH⋯π, and CH⋯π, CCl⋯CH and CH⋯CH interactions. The ionic strength in solution slightly affects the adsorption stability of neutral PPCPs, while the sorption of charged pollutants is enhanced. This mechanistic information provides quantitative data for a better understanding of the interactions between organic pollutants and MPs, serving as valuable information for sorption/kinetic studies.

The Role of Phorbol Diesters in Mediating Human Placental Aromatase Cytochrome P450 Activity

Due to the aromatase enzyme’s involvement in estrogen biosynthesis, aromatase inhibitors have emerged as the preferred treatment for postmenopausal women with ER+ breast cancer. Using computational chemistry tools, we investigate how the human placental aromatase cytochrome P450 interacts with various phorbols with distinct chains at C-12, C-13, and C-20, as well as the well-known aromatase inhibitors anastrozole, exemestane, and letrozole. To identify phorbol-aromatase interactions, we performed a protein–ligand docking using the structures of our ligands and proteins using the Flare software (version 2.0, Cresset Software, Litlington, UK). These preliminary findings show that the phorbols considered (P-12,13-diAcPh, P-12,13-diiBu, P-12AcPh-13iBu, P-12Ang-13iBu, P-20Ac-12AcPh-13iBu and P-20Ac-12Ang-13iBu) had the highest binding energies in comparison with the commercially available aromatase inhibitors (anastrozole, letrozole, exemestane) used in this study. A subset of the previously described binding residues of testosterone (TST), the endogenous ligand, were also found to be responsible for the phorbol diesters’ binding to the aromatase enzyme, as demonstrated by the findings. This further suggests that the phorbol diesters can bind efficiently to CYP19A1 and may be able to alter its activity because they had higher binding energies than the commercially available drugs.

MYOGLOBIN vs. HEMOGLOBIN BLOCKADE MODEL RELATED SMOKE GAS INHALATION - A COMPUTATIONAL ANALYSIS

To identify the pattern of myoglobin compared to hemoglobin blockade by the combustion products contained in the fire smoke using computational chemistry tools. The myoglobin unavailability can be a determining factor of the severity and consequences of smoke poisoning, generating the inability of patients to attempt evacuate themselves, compromising myocardial function, leading to crush syndrome-like effects and increasing of multi-organ failure to the victims of mass burn casualties event. In this study, it was used quantum chemical calculations performed with the Gaussian program suite using DFT/B3LYP/6-311G level of theory to optimize molecular geometries, calculate the molecular electrostatic potential, and obtain the vibrational spectrum. These calculations were applied to the myoglobin and hemoglobin model, thus studying their binding to the essential components of toxic fire smoke. Comparing the structural descriptors – frontier molecular orbitals, energy difference, electric dipole moment (μ), was obtained the highest values as belonging to hydrogen cyanide (2.9), which may explain its increased reactivity, meaning strong interaction with both myoglobin and hemoglobin, followed by hydrochloric acid (1.03) and carbon monoxide (0.122). Within the framework of complex intoxication generated by the inhalation of fire smoke, myoglobin is blocked in a temporal manner and according to a very similar pattern to hemoglobin. It follows that the significant rhabdomyolysis found in these patients is due not only to hypoxemia but also to the primary unavailability of myoglobin, and myocardial damage is also multifactorial. Although slightly discussed, the calculation of different structural and geometric descriptors for hydrochloric acid reveals for hydrochloric acid high values, suggesting binding affinities comparable to those of carbon monoxide. Molecular modeling programs allow for new approaches and can identify parameters or areas of their reference that influence the management of patients intoxicated with fire smoke components.

Solvent-free synthesis of protic ionic liquids. Synthesis, characterization and computational studies of triazolium based ionic liquids

A series of triazolium and imidazolium based protic ionic liquids were synthesized using a solvent-free method designed to address several limitations encountered with other commonly used methods. Using this method, pure (98–99% m/m) and dry (128–553 ppm of water) protic ionic liquids were synthesized (in a laboratory scale) without the need for purification methods that require heating the ionic liquid, hence avoiding the common issue of thermal decomposition. This method was also designed to allow for the accurate measurement of acid and base, and for the controlled mixing of both compounds, which is essential to avoid producing impure protic ionic liquids with excess of either acid or base. The system is constructed of only glass and chemically resistant polymer (PTFE and PVDF) parts, which avoid other contaminants that can result from unwanted reactions involving the reagents with common laboratory tools (metallic objects, paper, plastic, etc.). This process is described in detail in the paper as well as in a video. The resulting ionic liquids were carefully analyzed by spectroscopic and thermal methods designed to avoid water absorption, which is known to affect their properties. To complement this experimental characterization, computational chemistry tools were used to assess the ionic liquids’ properties, as well as to assign vibrational modes.

Amalgamation of comparative protein modeling with quantitative structure-retention relationship for prediction of the chromatographic behavior of peptides

Peptide therapeutics plays a prominent role in medical practice. Both peptides and proteins have been used in several disease conditions like diabetes, cancer, bacterial infections etc. The optimization of a peptide library is a time consuming and expensive chore. The tools of computational chemistry offer a way to optimize the properties of peptides. Quantitative Structure Retention (Chromatographic) Relationships (QSRR) is a powerful tool which statistically derives relationships between chromatographic parameters and descriptors that characterize the molecular structure of analytes. In this paper, we show how Comparative Protein ModelingQuantitative Structure Retention Relationship (acronym ComProM-QSRR) can be used to predict the retention time of peptide sequences. This formalism is founded on our earlier published QSAR methodology HomoSAR. ComProM-QSRR can recognize and distinguish the contribution of amino acids at specific positions in the peptide sequences to the retention phenomena through their related physicochemical properties. This study firmly establishes the fact that this approach can be pragmatically used to predict the retention time to all classes of peptides regardless of size or sequence.

Modeling Differential Enthalpy of Absorption of CO2 with Piperazine as a Function of Temperature.

Temperature-dependent correlations for equilibrium constants (ln K) and heat of absorption (ΔHabs) of different reactions (i.e., deprotonation, double deprotonation, carbamate formation, protonated carbamate formation, dicarbamate formation) involved in the piperazine (PZ)/CO2/H2O system have been calculated using computational chemistry based ln K values input to the Gibbs–Helmholtz equation. This work also presents an extensive study of gaseous phase free energy and enthalpy for different reactions using composite (G3MP2B3, G3MP2, CBS-QB3, and G4MP2) and density functional theory [B3LYP/6-311++G(d,p)] methods. The explicit solvation shell (ESS) model and SM8T solvation free energy coupled with gaseous phase density functional theory calculations give temperature-dependent reaction equilibrium constants for different reactions. Calculated individual and overall reaction equilibrium constants and enthalpies of different reactions involved in CO2 absorption in piperazine solution are compared against experimental data, where available, in the temperature range 273.15–373 K. Postcombustion CO2 capture (PCC) is a temperature swing absorption–desorption process. The enthalpy of the solution directly correlates with the steam requirement of the amine regeneration step. Temperature-dependent correlations for ln K and ΔHabs calculated using computational chemistry tools can help evaluate potential PCC solvents’ thermodynamics and cost-efficiency. These correlations can also be employed in thermodynamic models (e.g., e-UNIQUAC, e-NRTL) to better understand postcombustion CO2 capture solvent chemistry.