Quantitative Predictions and Experimental Validation of Liquid-Vapor Interfacial Tension in Binary and Ternary Mixtures of Alkanes Using Molecular Dynamics Simulations.

Liquid-vapor interfacial properties of alkane mixtures present a challenge for experimental determination, especially under conditions relevant to the energy industry processes. Molecular dynamics (MD) simulations can accurately predict interfacial tensions (IFTs) for complex alkane mixtures under virtually any conditions, thereby alleviating the need for difficult and costly experiments. MD simulations with the CHARMM force field and empirical corrections for the IFT and pressure were used to obtain the IFT for three binary mixtures of ethane (with n-pentane, n-hexane, and n-nonane) and a ternary system (ethane/n-butane/n-decane) under a variety of conditions. The results were thoroughly validated against experimental data from the literature, and new original IFT data were collected using the pendant drop method. The simulations are able to reproduce the experimental IFT to better than 0.5 mN/m or 5% on average and within 1 mN/m or 10% in the worst case. IFTs for the studied three binary and ternary alkane mixtures were predicted for wide ranges of conditions with no known experimental data. Finally, using the MD simulation data, the reliability of the widely used empirical parachor model for predicting IFT was reaffirmed, and the significance of the empirical parameters examined to establish an optimal balance between the accuracy and broad applicability of the model.

Wettability reversal on oil-wet calcite surfaces: Experimental and computational investigations of the effect of the hydrophobic chain length of cationic surfactants.

HYPOTHESIS: Oil recovery from carbonate reservoirs is often low, in a large part due to the oil-wet state of the constituent rocks. Cationic surfactants are among the most effective compounds capable of reversing the carbonate wettability to more water-wet, which significantly enhances oil recovery. Screening for the most effective cationic surfactants can be facilitated by studying the effects of specific molecular properties, such as the hydrophobic chain length, on the wettability reversal efficiency using molecular dynamics (MD) simulations. EXPERIMENTS AND SIMULATIONS: Wettability reversal by quaternary ammonium cationic surfactants with varying hydrophobic chain length was studied by the combination of MD simulation and experimental contact angle measurements on oil-wet calcite chips. Both experiments and simulations also featured model oils consisting of different size hydrocarbons in order to explore the potential size-specific interactions between the surfactants and oil molecules. FINDINGS: We found strong correlation between the wettability reversal and the surfactant length, with the longer surfactants universally rendering calcite surfaces more water-wet. By contrast, the wettability reversal is independent of the model oil used, implying that the effect is not due to specific hydrocarbon size. Instead, the superior wettability reversal performance of the more hydrophobic surfactants is due to their greater affinity to the oil/brine interfaces.

Liquid-Vapor Interfacial Tension in Alkane Mixtures: Improving Predictive Capabilities of Molecular Dynamics Simulations.

The liquid-vapor interfacial properties of hydrocarbons and their mixtures are important factors in a wide range of industrial processes and applications. Determining these properties experimentally, however, is not only practically demanding, but many important properties, such as phase densities and compositions are not directly experimentally accessible, thus requiring the development of theoretical models. Molecular dynamics (MD) simulations, by contrast, are relatively straightforward even for the most complex of mixtures and directly provide all of the microscopic quantities for the studied systems. We have previously applied MD simulations to study the liquid-vapor equilibria of mixtures of hydrocarbons and CO2 that are particularly relevant to hydrocarbon recovery from geologic formations. In this study, we explore in more detail the robustness of the simulation methods with respect to the choice of the model system parameters, investigate the accuracy of the simulations in determining the key quantities: system pressure and interfacial tension (IFT), and, finally, devise a simple correction for achieving a much closer agreement between the simulated and experimental quantities. We perform extensive MD simulations for three mixtures, propane/n-pentane, propane/n-hexane, and CO2/n-pentane, using model systems from 1000 up to 100 000 molecules, and different simulation box dimensions to test for the sensitivity to finite-size effects. The results show that changing the system size and box dimensions does not significantly impact the accuracy of the simulations. Subsequently, we examine the accuracy of the MD simulations in determining the pressure and IFT for two pure hydrocarbon systems, n-pentane and n-heptane. Finally, we propose a simple linear correction formula for the pressures and IFTs obtained from the MD simulations that closely reproduce the experimental values for single components and mixtures of hydrocarbons. Our results enable the MD simulations to provide more accurate and reliable predictions of the interfacial properties, thereby reducing the need for challenging laboratory experiments.

Surfactant-induced wettability reversal on oil-wet calcite surfaces: Experimentation and molecular dynamics simulations with scaled-charges.

HYPOTHESIS: Surfactant flooding is the leading approach for reversing the wettability of oil-wet carbonate reservoirs, which is critical for the recovery of the remaining oil. Combination of molecular dynamics (MD) simulations with experiments on simplified model systems can uncover the molecular mechanisms of wettability reversal and identify key molecular properties for systematic design of new, effective chemical formulations for the enhanced oil recovery. EXPERIMENTS/SIMULATIONS: Wettability reversal by a series of surfactant solutions was studied experimentally using contact angle measurements on aged calcite chips, and a novel MD simulation methodology with scaled-charges that provides superior description of the ionic interactions in aqueous solutions. FINDINGS: The MD simulation results were in excellent agreement with the experiments. Cationic surfactants were the most effective in reversing the calcite wettability, resulting in complete detachment of the oil from the surface. Some nonionic surfactants also altered the wettability, but to a lesser degree, while the amphoteric and anionic surfactants had no effect. From the tested cationic surfactants, the double-tailed one was the least effective, but the experiments were inconclusive due to its poor solubility. Contributions of specific interactions to the wettability reversal process and implications for the design and optimization of surfactants for the enhanced oil recovery are discussed.

Multi-Probe Equilibrium Analysis of Gradual (Un)Folding Processes.

Studies of small proteins that exhibit noncooperative, gradual (un)folding can offer unique insights into the rarely accessible intermediate stages of the protein folding processes. Detailed experimental characterization of these intermediate states requires approaches that utilize multiple site-specific probes of the local structure. Isotopically edited infrared (IR) spectroscopy has emerged as a powerful methodology capable of providing such high-resolution structural information. Labeling of selected amide carbonyls with 13C results in detectable side-bands of amide I' vibrations, which are sensitive to local conformation and/or solvent exposure without introducing any significant structural perturbation to the protein. Incorporation of isotopically labeled amino acids at specific positions can be achieved by the chemical synthesis of the studied proteins. We describe the basic procedures for synthesis of 13C isotopically edited protein samples, experimental IR spectroscopic measurements and analysis of the site-specific equilibrium thermal unfolding of a small protein from the temperature-dependent IR data.

Double Hydrogen Bonding Dimerization Propensity of Aqueous Hydroxy Acids Investigated Using Vibrational Optical Activity.

Lactic and malic acids are key substances in a number of biochemical processes in living cells and are also utilized in industry. Vibrational spectroscopy represents an efficient and sensitive way to study their structure and interactions. Since water is the natural environment, proper understanding of their molecular dynamics in aqueous solutions is of critical importance. To this end, we employed Raman spectroscopy and Raman optical activity (ROA) to study the conformation of l-lactic and l-malic acids in water (while varying pH, temperature, and concentration), with special emphasis on their double hydrogen bonding dimerization propensity. Raman and ROA experimental data were supported by extensive theoretical calculations of the vibrational properties and by additional experiments (IR absorption, vibrational circular dichroism, and NMR). Conformational behavior of the acids in water was described by molecular dynamics simulations. Reliability of the results was verified by calculating the vibrational properties of populated conformers and by comparing thus obtained spectral features with the experimental data. Calculations estimated the incidence of H-bonded dimers in water to be low in lactic acid and comparable to monomers in malic acid. The "hybrid" approach presented here reveals limitations of relying on the experimental spectra alone to study dimer formation.

Molecular Dynamics Simulations of the Vapor-Liquid Equilibria in CO2/n-Pentane, Propane/n-Pentane, and Propane/n-Hexane Binary Mixtures.

Molecular dynamics (MD) simulations were used to study vapor-liquid equilibrium interfacial properties of n-alkane and n-alkane/CO2 mixtures over a wide range of pressure and temperature conditions. The simulation methodology, based on CHARMM molecular mechanics force field with long-range Lennard-Jones potentials, was first validated against experimental interfacial tension (IFT) data for two pure n-alkanes (n-pentane and n-heptane). Subsequently, liquid-vapor equilibria of CO2/n-pentane, propane/n-pentane, and propane/n-hexane mixtures were investigated at temperatures from 296 to 403 K and pressures from 0.2 to 6 MPa. The IFT, liquid and vapor phase densities, and molecular compositions of the liquid and vapor phases and of the interface were analyzed. The calculated mixture IFTs were in excellent agreement with experiments. Likewise, calculated phase densities closely matched values obtained from the equation of state (EOS) fitted to the experimental data. Examination of the density profiles, particularly in the liquid-vapor transition regions, provided a molecular-level rationalization for the observed trends in the IFT as a function of both molecular composition and temperature. Finally, two variants of the empirical parachor model commonly used for predicting the IFT, the Weinaug-Katz and Hugill-Van Welsenes equations, were tested for their accuracy in reproducing the MD simulation results. The IFT prediction accuracies of both equations were nearly identical, implying that the simpler Weinaug-Katz model is sufficient to describe the IFT of the studied systems.

Wettability Reversal on Dolomite Surfaces by Divalent Ions and Surfactants: An Experimental and Molecular Dynamics Simulation Study.

Due to the importance of the dolomite mineral in carbonate reservoirs, the wettability characteristics of dolomite surfaces were studied with both experiments and molecular dynamics simulations. Contact angle measurements confirm that the dolomite surface can be rendered oil-wet by carboxylates (acidic components of crude oil) and that the cationic surfactant can reverse the oil-wetness more effectively than the anionic surfactant used in this study. The oil-wetness of an aged dolomite chip was reduced when treated with MgSO4 solution at 80 °C, while CaCl2, MgCl2, and Na2SO4 solutions did not produce any significant wettability alteration. The effects of surfactants and divalent ions, Ca2+, Mg2+, and SO42- (also referred to as Smart Water ions), were simulated with two model dolomite surfaces containing point defects and step vacancies, respectively. The results indicate that the cationic surfactant can weaken the attraction between the oil phase and the carboxylates, while the anionic surfactant tends to maintain the oil-wetness of the dolomite surface by replacing the carboxylates through competitive adsorption. All Ca2+, Mg2+, and SO42- ions can act as potential determining ions, and the detachment of carboxylates is due to the repulsion from SO42- ions drawn close to the surface in the presence of adsorbed Mg2+.

Effects of Surfactant Charge and Molecular Structure on Wettability Alteration of Calcite: Insights from Molecular Dynamics Simulations.

Wettability alteration of oil-wet calcite by surfactants was studied by means of molecular dynamics (MD) simulations. The simulations use the recently developed model for positively charged calcite surface, whose oil-wet state originates from binding of negatively charged carboxylate molecules contained in the oil, consistently with the bulk of the available experimental data. The ability to alter the surface wettability, which can be directly quantified by the release of the surface-bound carboxylates, is tested for nine different surfactants of all charge types-cationic, anionic, nonionic, and zwitterionic-and compared to that of brine. It was found that only the cationic surfactants are able to detach the organic carboxylates more efficiently than brine, while the neutral and anionic surfactants do not seem to have any measurable effect on the wettability. The outperformance of the cationic surfactants is generally consistent with the majority of previously published experimental observations. The data also point toward a consistently better performance of single-tailed cationic surfactants over the two-tailed structure. Molecular mechanism of the wettability alteration by different types of surfactants is discussed, along with the implications of the results for the design of new surfactant formulations for the enhanced oil recovery.

A positively charged calcite surface model for molecular dynamics studies of wettability alteration.

A new model for a positively charged calcite surface was developed to allow realistic molecular dynamics studies of wettability alteration on carbonate rocks. The surface charge was introduced in a manner consistent with the underlying calcite geochemistry and with the conclusions of recent quantum mechanical studies. The simulations using the new surface model demonstrate that the experimentally observed wettability behavior of calcite is represented correctly. In particular, the model surface became oil-wet due to the adsorption of the carboxylate species. Furthermore, the oil-wet conditions were reversed more effectively by a cationic surfactant than by an anionic one, in agreement with the majority of experimental observations. Finally, with simulated smart water, the well-documented wettability alteration abilities of Ca2+ and SO42- could be explained by the formation of ion-pairs and competitive adsorption onto the surface, respectively. The simulation results with the new surface model conceptually agree with the electric double layer expansion being the predominant mechanism for the low salinity effect in oil recovery enhancement. The proposed calcite surface model will benefit future simulation studies on the wettability characteristics of carbonate rocks, and facilitate the design and optimizations of chemical agents and formulations to enhance the oil recovery from carbonate reservoirs.

Hydrogen gas formation from the photolysis of rhenium hydrides - mechanistic and computational studies.

The photolysis of 4,4'-disubstituted, 2,2'-bipyridine fac-Re(bpy)(CO)3H derivatives produces stoichiometric H2 gas. The rate of production varies greatly depending on the electronic nature of the disubstituted bipyridine (bpy) with halogenated substituents increasing the rate. Isotope labeling studies along with B3LYP geometry optimization DFT modeling studies indicate a mechanism involving a Re-H-Re bridging complex that leads to a dimeric Re-Re(η2-H2) state prior to dissociating H2 gas.

Effect of Mutations on the Global and Site-Specific Stability and Folding of an Elementary Protein Structural Motif.

Understanding the folding mechanism of proteins requires detailed knowledge of the roles of individual amino acid residues in stabilization of specific elements and local segments of the native structure. Recently, we have utilized the combination of circular dichroism (CD) and site-specific 13C isotopically edited infrared spectroscopy (IR) coupled with the Ising-like model for protein folding to map the thermal unfolding at the residue level of a de novo designed helix-turn-helix motif αtα. Here we use the same methodology to study how the sequence of local thermal unfolding is affected by selected mutations introduced into the most and least stable parts of the motif. Seven different mutants of αtα are screened to find substitutions with the most pronounced effects on the overall stability. Subsequently, thermal unfolding of two mutated αtα sequences is studied with site-specific resolution, using four distinct 13C isotopologues of each. The data are analyzed with the Ising-like model, which builds on a previous parametrization for the original αtα sequence and tests different ways of incorporating the amino acid substitution. We show that for both more and less stable mutants only the adjustment of all interaction parameters of the model can yield a satisfactory fit to the experimental data. The stabilizing and destabilizing mutations result, respectively, in a similar increase and decrease of the stability of all probed local segments, irrespective of their position with respect to the mutation site. Consequently, the relative order of their unfolding remains essentially unchanged. These results underline the importance of the interconnectivity of the stabilizing interaction network and cooperativity of the protein structure, which is evident even in a small motif with apparently noncooperative, heterogeneous unfolding. Overall, our findings are consistent with the native structure being the dominant factor in determining the folding mechanism, regardless of the details of its overall or local thermodynamic stabilization.

Solid Parahydrogen Infrared Matrix Isolation and Computational Studies of Lin-(C2H4)m Complexes.

Complexes of lithium atoms with ethylene have been identified as potential hydrogen storage materials. As a Li atom approaches an ethylene molecule, two distinct low-lying electronic states are established; one is the 2A1 electronic state (for C2v geometries) that is repulsive but supports a shallow van der Waals well and correlates with the Li 2s atomic state, and the second is a 2B2 electronic state that correlates with the Li 2p atomic orbital and is a strongly bound charge-transfer state. Only the 2B2 charge-transfer state would be advantageous for hydrogen storage because the strong electric dipole created in the Li-(C2H4) complex due to charge transfer can bind molecular hydrogen through dipole-induced dipole and dipole-quadrupole electrostatic interactions. Ab initio studies have produced conflicting results for which electronic state is the true ground state for the Li-(C2H4) complex. The most accurate ab initio calculations indicate that the 2A1 van der Waals state is slightly more stable. In contrast, argon matrix isolation experiments have clearly identified the Li-(C2H4) complex exists in the 2B2 state. Some have suggested that argon matrix effects shift the equilibrium toward the 2B2 state. We report the low-temperature synthesis and IR characterization of Lin-(C2H4)m (n = 1, m = 1 and 2) complexes in solid parahydrogen which are observed using the C═C stretching vibration of ethylene in the complex. These results show that under cryogenic hydrogen storage conditions the Li-(C2H4) complex is more stable in the 2B2 electronic state and thus constitutes a potential hydrogen storage material with desirable characteristics.

A new parameter-rich structure-aware mechanistic model for amino acid substitution during evolution.

Improvements in the description of amino acid substitution are required to develop better pseudo-energy-based protein structure-aware models for use in phylogenetic studies. These models are used to characterize the probabilities of amino acid substitution and enable better simulation of protein sequences over a phylogeny. A better characterization of amino acid substitution probabilities in turn enables numerous downstream applications, like detecting positive selection, ancestral sequence reconstruction, and evolutionarily-motivated protein engineering. Many existing Markov models for amino acid substitution in molecular evolution disregard molecular structure and describe the amino acid substitution process over longer evolutionary periods poorly. Here, we present a new model upgraded with a site-specific parameterization of pseudo-energy terms in a coarse-grained force field, which describes local heterogeneity in physical constraints on amino acid substitution better than a previous pseudo-energy-based model with minimum cost in runtime. The importance of each weight term parameterization in characterizing underlying features of the site, including contact number, solvent accessibility, and secondary structural elements was evaluated, returning both expected and biologically reasonable relationships between model parameters. This results in the acceptance of proposed amino acid substitutions that more closely resemble those observed site-specific frequencies in gene family alignments. The modular site-specific pseudo-energy function is made available for download through the following website: https://liberles.cst.temple.edu/Software/CASS/index.html.

Double Hydrogen Bonding between Side Chain Carboxyl Groups in Aqueous Solutions of Poly (ß-L-Malic Acid): Implication for the Evolutionary Origin of Nucleic Acids.

The RNA world hypothesis holds that in the evolutionary events that led to the emergence of life RNA preceded proteins and DNA and is supported by the ability of RNA to act as both a genetic polymer and a catalyst. On the other hand, biosynthesis of nucleic acids requires a large number of enzymes and chemical synthesis of RNA under presumed prebiotic conditions is complicated and requires many sequential steps. These observations suggest that biosynthesis of RNA is the end product of a long evolutionary process. If so, what was the original polymer from which RNA and DNA evolved? In most syntheses of simpler RNA or DNA analogs, the D-ribose phosphate polymer backbone is altered and the purine and pyrimidine bases are retained for hydrogen bonding between complementary base pairs. However, the bases are themselves products of complex biosynthetic pathways and hence they too may have evolved from simpler polymer side chains that had the ability to form hydrogen bonds. We hypothesize that the earliest evolutionary predecessor of nucleic acids was the simple linear polyester, poly (ß-D-malic acid), for which the carboxyl side chains could form double hydrogen bonds. In this study, we show that in accord with this hypothesis a closely related polyester, poly (ß-L-malic acid), uses carboxyl side chains to form robust intramolecular double hydrogen bonds in moderately acidic solution.

CdSe Quantum Dots Functionalized with Chiral, Thiol-Free Carboxylic Acids: Unraveling Structural Requirements for Ligand-Induced Chirality.

Functionalization of colloidal quantum dots (QDs) with chiral cysteine derivatives by phase-transfer ligand exchange proved to be a simple yet powerful method for the synthesis of chiral, optically active QDs regardless of their size and chemical composition. Here, we present induction of chirality in CdSe by thiol-free chiral carboxylic acid capping ligands (l- and d-malic and tartaric acids). Our circular dichroism (CD) and infrared experimental data showed how the presence of a chiral carboxylic acid capping ligand on the surface of CdSe QDs was necessary but not sufficient for the induction of optical activity in QDs. A chiral bis-carboxylic acid capping ligand needed to have three oxygen-donor groups during the phase-transfer ligand exchange to successfully induce chirality in CdSe. Intrinsic chirality of CdSe nanocrystals was not observed as evidenced by transmission electron microscopy and reverse phase-transfer ligand exchange with achiral 1-dodecanethiol. Density functional theory geometry optimizations and CD spectra simulations suggest an explanation for these observations. The tridentate binding via three oxygen-donor groups had an energetic preference for one of the two possible binding orientations on the QD (111) surface, leading to the CD signal. By contrast, bidentate binding was nearly equienergetic, leading to cancellation of approximately oppositely signed corresponding CD signals. The resulting induced CD of CdSe functionalized with chiral carboxylic acid capping ligands was the result of hybridization of the (achiral) QD and (chiral) ligand electronic states controlled by the ligand's absolute configuration and the ligand's geometrical arrangement on the QD surface.

Activation Strain Analysis of SN2 Reactions at C, N, O, and F Centers.

Fundamental principles that determine chemical reactivity and reaction mechanisms are the very foundation of chemistry and many related fields of science. Bimolecular nucleophilic substitutions (SN2) are among the most common and therefore most important reaction types. In this report, we examine the trends in the SN2 reactions with respect to increasing electronegativity of the reaction center by comparing the well-studied backside SN2 Cl- + CH3Cl with similar Cl- substitutions on the isoelectronic series with the second period elements N, O, and F in place of C. Relativistic (ZORA) DFT calculations are used to construct the gas phase reaction potential energy surfaces (PES), and activation strain analysis, which allows decomposition of the PES into the geometrical strain and interaction energy, is employed to analyze the observed trends. We find that SN2@N and SN2@O have similar PES to the prototypical SN2@C, with the well-defined reaction complex (RC) local minima and a central barrier, but all stationary points are, respectively, increasingly stable in energy. The SN2@F, by contrast, exhibits only a single-well PES with no barrier. Using the activation strain model, we show that the trends are due to the interaction energy and originate mainly from the decreasing energy of the empty acceptor orbital (σ*A-Cl) on the reaction center A in the order of C, N, O, and F. The decreasing steric congestion around the central atom is also a likely contributor to this trend. Additional decomposition of the interaction energy using Kohn-Sham molecular orbital (KS-MO) theory provides further support for this explanation, as well as suggesting electrostatic energy as the primary reason for the distinct single-well PES profile for the FCl reaction.

Chirality Inversion of CdSe and CdS Quantum Dots without Changing the Stereochemistry of the Capping Ligand.

L-cysteine derivatives induce and modulate the optical activity of achiral cadmium selenide (CdSe) and cadmium sulfide (CdS) quantum dots (QDs). Remarkably, N-acetyl-L-cysteine-CdSe and L-homocysteine-CdSe as well as N-acetyl-L-cysteine-CdS and L-cysteine-CdS showed "mirror-image" circular dichroism (CD) spectra regardless of the diameter of the QDs. This is an example of the inversion of the CD signal of QDs by alteration of the ligand's structure, rather than inversion of the ligand's absolute configuration. Non-empirical quantum chemical simulations of the CD spectra were able to reproduce the experimentally observed sign patterns and demonstrate that the inversion of chirality originated from different binding arrangements of N-acetyl-L-cysteine and L-homocysteine-CdSe to the QD surface. These efforts may allow the prediction of the ligand-induced chiroptical activity of QDs by calculating the specific binding modes of the chiral capping ligands. Combined with the large pool of available chiral ligands, our work opens a robust approach to the rational design of chiral semiconducting nanomaterials.

Sequence, structure, and cooperativity in folding of elementary protein structural motifs.

Residue-level unfolding of two helix-turn-helix proteins--one naturally occurring and one de novo designed--is reconstructed from multiple sets of site-specific (13)C isotopically edited infrared (IR) and circular dichroism (CD) data using Ising-like statistical-mechanical models. Several model variants are parameterized to test the importance of sequence-specific interactions (approximated by Miyazawa-Jernigan statistical potentials), local structural flexibility (derived from the ensemble of NMR structures), interhelical hydrogen bonds, and native contacts separated by intervening disordered regions (through the Wako-Saitô-Muñoz-Eaton scheme, which disallows such configurations). The models are optimized by directly simulating experimental observables: CD ellipticity at 222 nm for model proteins and their fragments and (13)C-amide I' bands for multiple isotopologues of each protein. We find that data can be quantitatively reproduced by the model that allows two interacting segments flanking a disordered loop (double sequence approximation) and incorporates flexibility in the native contact maps, but neither sequence-specific interactions nor hydrogen bonds are required. The near-identical free energy profiles as a function of the global order parameter are consistent with expected similar folding kinetics for nearly identical structures. However, the predicted folding mechanism for the two motifs is different, reflecting the order of local stability. We introduce free energy profiles for "experimental" reaction coordinates--namely, the degree of local folding as sensed by site-specific (13)C-edited IR, which highlight folding heterogeneity and contrast its overall, average description with the detailed, local picture.