Changes In Intermolecular Forces Research Articles

Significantly enhanced specific activity of Bacillus subtilis (2,3)-butanediol dehydrogenase through computer-aided refinement of its substrate-binding pocket

(2,3)-Butanediol dehydrogenases (BDHs) are widely utilized for the stereoselective interconversion between α-hydroxy ketones and vicinal diols to produce various functional building blocks. In this study, to enhance the specific activity towards (R)-phenyl-1,2-ethanediol (1a) for 2-hydroxyacetophenone (1b), the substrate-binding pocket of a Bacillus subtilis BDH (BsBDHA) was refined through site-directed mutagenesis. Based on molecular docking simulations, 14 residues were identified and subjected to alanine scanning mutagenesis. After screening, two residues, His42 and Gly292, were singled out for partial site-saturation mutagenesis. The results revealed that BsBDHAH42A and BsBDHAG292A displayed high activities of 3.21 and 1.97 U/mg, respectively. Employing combinatorial mutagenesis, a superior mutant, BsBDHAI49L/V266L/G292A, was developed, exhibiting significantly enhanced specific activity and catalytic efficiency towards (R)-1a, achieving 14.81 U/mg and 4.47 mM−1 s−1, respectively, which were 27.4- and 55.9-fold higher than those of BsBDHA. Further substrate spectrum analysis revealed that the superior mutant displayed increased specific activities for (R)-2a–6a by 1.4- to 10.3-fold. The integration of BsBDHAI49L/V266L/G292A into a three-enzymatic cascade for the synthesis of 1b effectively elevated the yield from 58.1 to 82.4%. Molecular mechanism analysis indicated that the mutation-induced changes in intermolecular forces resulted in a higher frequency of reactive conformations for (R)-1a in BsBDHAI49L/V266L/G292A compared to BsBDHA.

Binary imidazolium based aqueous ionic liquid droplet on a rough surface: a molecular dynamics study

Ionic liquids (ILs) have garnered immense attention due to their tunable physicochemical properties. In this study, we delve into the wetting behaviour and interfacial properties of aqueous binary IL mixtures containing [EMIM] [BF4] and [HMIM] [BF4] on both smooth and rough graphite surfaces. Employing classical molecular dynamics simulations, we systematically explored the effects of IL concentration and surface morphology on wetting phenomena. To ensure the equilibrium of the systems, we began by calculating the interaction energies between the components. Subsequently, contact angles were computed, shedding light on the wetting characteristics of the aqueous binary IL mixtures. We meticulously examined the density profiles of the IL systems from the substrate to unravel the dominance of one IL over the other, exploiting the hydrophilic nature of [EMIM] [BF4] and the hydrophobic nature of [HMIM] [BF4]. A comprehensive analysis of hydrogen bond distribution allowed us to discern the intricate nature of these aqueous binary IL droplets. We probed the changes in intermolecular forces within the aqueous IL solution by investigating surface tensions. The tunability of these ILs emerges as a significant aspect of our study, paving the way for their tailored application in engineering and scientific domains. Schematic diagram showing the density distribution of hydrophilic and hydrophobic ILs ([EMIM] [BF4] and [HMIM] [BF4]) in water and also the hydrogen bond (HB) distribution of anion ([BF4]−) water inside the droplet on a pillared surface with a surface fraction ( f ) of 0.4 and pillar height of H = 4 .

Effect of chlorogenic acid on lotus seed starch gelatinization behavior and complexation mode during microwave treatment

The pasting behavior and changes in intermolecular forces were compared between microwave (MW)- and hydrothermal (hot water; HT)-treated chlorogenic acid (CA)/lotus seed starch (LS)/water mixtures, by rheological, spectroscopic and microscopic analysis. MW treatment directly heated polar molecules throughout the starch granules producing even heating, compared with HT treatment in which heat transfer was limited to conduction from the granule surface. MW treatment more rapidly disrupted the starch double helical structure and liberated many starch chains that formed larger amounts of a non-covalent inclusion complex with CA than HT treatment. In addition, MW treatment produced a coating of LS-CA complex on the starch granule surface which modified the pasting properties of the starch. The LS-CA complex had a denser structure than LS, which enhanced the thermal stability and crystalline water binding capacity of LS. The non-covalent complexes were stabilized by hydrogen bonding and electrostatic interactions between starch chains, hydrophobic interactions between the caffeic acid residue in CA to the starch chain hydrophobic helical cavity and attraction of the hydroxyl groups at the reducing end of the LS chains to the H+ on the CA (electrostatic interaction). Of these, hydrogen bonding and electrostatic interactions were the main intermolecular forces between LS chains. These findings contribute to clarification of the mechanism of action of polyphenols on the starch gelatinization process and will help to improve the formulation of functional starch products.

Throwing and manipulating and cheating with a DNA nano-dice

Artificial molecular machines have captured the imagination of researchers, given their clear potential to mimic and influence human life. Key to behavior simulation is to reproduce the specific properties of physical or abstract systems. Dice throwing, as a stochastic model, is commonly used for result judgment or plan decision in real life. In this perspective we utilize DNA cube framework for the design of a dice device at the nanoscale to reproduce probabilistic events in different situations: equal probability, high probability, and low probability. We first discuss the randomness of DNA cube, or dice, adsorbing on graphene oxide, or table, and then explore a series of events that change the probability through the way in which the energy released from entropy-driven strand displacement reactions or changes in intermolecular forces. As such, the DNA nano-dice system provides guideline and possibilities for the design, engineering, and quantification of behavioral probability simulation, a currently emerging area of molecular simulation research.

Assessment of CO2-Oil swelling behavior using molecular dynamics simulation: CO2 utilization and storage implication

CO2 injection into petroleum reservoirs is an effective enhanced oil recovery (EOR) method that can increase the recovery of oil while reducing CO2 emissions into the atmosphere. To ensure successful implementation of CO2 EOR, a detailed understanding of reservoir fluid properties and the phase behavior of CO2-oil mixtures at different scales is required. The extent to which CO2 injection improves the oil recovery factor is heavily dependent on the swelling behavior of CO2-oil mixtures, which can be quantified by swelling factors. In this study, we model a CO2-oil swelling test using molecular dynamics (MD) simulations to calculate the swelling factors over a pressure range of 24.8 to 68 bar at a temperature of 303.15 K for an actual crude oil sample. The multicomponent molecular model of the oil is built using 1000 molecules of six hydrocarbons, based on the compositional analysis of the oil sample. CO2 molecules are then added to the system at several pressure steps, based on experimental CO2 solubility data, and the resulting swelling factors are compared to their corresponding experimental values. The results of this study demonstrate that the MD simulation model can be successfully used to investigate CO2-oil swelling behavior and accurately predict the swelling factors with a minor mean percentage error of 6%. Additionally, analysis of potential energy variations due to interactions between different molecules in the system under increasing pressures and CO2 mole fractions indicates that the swelling process is primarily controlled by changes in intermolecular forces between CO2-oil and oil-oil molecular pairs, while the effect of CO2-CO2 molecular potentials on oil swelling is minimal. This work highlights the ability of the MD simulation technique to model the complex phase behavior of CO2-oil mixtures and provides unique insights into the molecular-scale mechanisms of CO2 dissolution in oil and the resulting swelling phenomenon.

Long-term hygroscopic dimensional changes of core buildup materials in deionized water and artificial saliva.

The dimensional stability of core buildup materials plays an important role in clinical application. In this study, hygroscopic dimensional changes of four commercial core buildup materials were investigated in deionized water and artificial saliva for up to 150 days. Specimens were made within a customized cylindrical mold. The initial mass and the apparent mass in liquids were measured. All the tested materials showed hygroscopic expansion after a 150-days immersion time. Hygroscopic expansion of these four materials can partly compensate for the polymerization shrinkage. SDR showed the lowest hygroscopic expansion of the four tested materials when immersed in deionized water and artificial saliva. PC showed the highest hygroscopic expansion in deionized water, while LC showed the highest hygroscopic expansion in artificial saliva. In the case of different immersion solvents, osmotic pressure should be considered. For hygroscopic dimensional changes, the hydrophilicity of monomers and changes of intermolecular forces may be crucial factors.

Molecular forces and gelling properties of heat-induced gel from egg white protein glycated with isomalto-oligosaccharide

Glycation with fructo-oligosaccharide (FO) and isomalto-oligosaccharide (IMO) was employed to improve the heat-induced egg white protein (EWP) gels. Results showed that EWP glycated with IMO exhibited a greater degree of glycation (DG) and better gelling properties than those of FO-EWP conjugates. The electrophoresis and liquid chromatography mass spectrometry (LC-MS) indicated that IMO was successfully covalently cross-linked with EWP. Fourier transform infrared spectroscopy (FTIR) showed that the glycation increased the percentages of intramolecular and intermolecular β-sheets of EWP and lowered the contents of 310-helical structure. The rheological test indicated that the gel-forming temperature of EWP was brought forward with the increase of glycation time. Furthermore, the glycation could induce the formation of EWP gel characterized by the higher strength of hydrogen bonds and hydrophobic interactions and lower strength of disulfide bonds. The changes of intermolecular forces resulted in a fine network structure of EWP gel, which significantly enhanced the fracture strength, bound water relaxation proportion and water-holding capacity (WHC) of the gel. A positive correlation existed in the WHC and gel fracture strength. This study proved that glycation with IMO efficiently improved the gelling properties of EWP.

Effects of tea polyphenol and Ca(OH)2 on the intermolecular forces and mechanical, rheological, and microstructural characteristics of duck egg white gel

This study investigates the effects of tea polyphenol (TP) and Ca(OH)2 on the physicochemical, mechanical, rheological, and microstructural characteristics of alkali-induced duck egg white (EW) gels. The surface hydrophobicity increases significantly after adding TP, while decreases after adding Ca(OH)2. Secondary structural analysis indicates that the addition of TP and Ca(OH)2 reduces the β-sheets content and increases the ɑ-helical content. The addition of TP improves the interaction of nonspecific cross-linking but weakens other forces, and the interactions in EW gel are mainly supported by hydrogen bonds and hydrophobic interactions under the influence of Ca(OH)2. The results of electrophoresis show that crosslinked proteins are formed and the protection provided by TP reduces protein degradation. The addition of a high proportion of TP reduces the storage modulus (G′) of EW gel, decreasing its rigidity and mechanical properties, such as hardness and rupture strength. However, after adding Ca(OH)2, the storage modulus increases gradually and the mechanical strength of EW gel increases, which might be related to the formation of calcium bridges. Scanning electron microscopy indicates that three-dimensional network structures are formed when TP is added, while granular or clustered structures are generated by Ca(OH)2 addition. Correlation analysis shows that the physical properties of EW gel are related to changes in intermolecular forces and the microenvironment, especially pH and nonspecific cross-linking. These results suggest that the addition of TP and Ca(OH)2 affects the physicochemical properties of EW gel differently, which were mainly attributed to the effects of molecular interaction and micro-environment.

Insights into Glycol Ether-Alkanol Mixtures from a Combined Experimental and Theoretical Approach.

The binary liquid mixtures of glycol ethers (glymes) + 1-alkanol were characterized from the microscopic and macroscopic viewpoints through a combined experimental and theoretical study. Structuring, dynamics, and intermolecular forces were determined using density functional theory and classical molecular dynamics methods. The macroscopic behavior was studied though the measurement of relevant physicochemical properties and Raman IR studies. The changes in intermolecular forces with mixture composition, temperature, and the effects from the types of glymes as well as 1-alkanols were considered. Hydrogen bonding in the mixed fluids, its changes upon mixing, and mixture composition showed a large effect on fluids' structure and determined most of the fluids' properties together with the presence of hydrophobic domains from long 1-alkanols.

Length-dependent self-assembly of oligothiophene derivatives in thin films

Abstract

Chemomechanics of Surface Stresses Induced by DNA Hybridization

When biomolecular reactions occur on one surface of a microcantilever beam, changes in intermolecular forces create surface stresses that bend the cantilever. While this phenomenon has been exploited to create label-free biosensors and biomolecular actuators, the mechanisms through which chemical free energy is transduced to mechanical work in such hybrid systems are not fully understood. To gain insight into these mechanisms, we use DNA hybridization as a model reaction system. We first show that the surface grafting density of single-stranded probe DNA (sspDNA) on a surface is strongly correlated to its radius of gyration in solution, which in turn depends on its persistence length and the DNA chain length. Since the persistence length depends on ionic strength, the grafting density of sspDNA can be controlled by changing a solution's ionic strength. The surface stresses produced by the reaction of complementary single-stranded target DNA (sstDNA) to sspDNA depend on the length of DNA, the grafting density, and the hybridization efficiency. We, however, observe a remarkable trend: regardless of the length and grafting density of sspDNA, the surface stress follows an exponential scaling relation with the density of hybridized sspDNA.

The effect of molecular excitation on crystal packing. 9-Cyano- and 9,10-dimethylanthracene as excited guest/host and host/guest pairs

Abstract The crystal packing of an electronically excited 9-cyanoanthracene (9-CNA) in host 9,10-dimethylanthracene (DMA), and the packing with roles of host and guest exchanged, are calculated using standard atom-atom potentials and a range of estimates of the changes in intermolecular forces in the molecular excited states. Exciplex formation is discussed in the two cases. Excited 9-CNA in DMA is stable to unsymmetrical displacement: both in the unrelaxed and relaxed lattices. Excited DMA is unstable in a rigid 9-CNA lattice, being asymmetrically displaced towards one neighbour in the molecule stack; however, since the excitation of DMA is at higher energy than that of 9-CNA, the physically more realistic case is that of an excited 9-CNA molecule adjacent to the guest. Calculation shows that the excited molecule, in a rigid lattice, is unstable at its ground-state site, and that it will move to one of two potential minima closer to either the neighbour DMA or to the other neighbour (9-CNA). However, the simulation of long-time behaviour through calculation of changes in local molecular packing suggests no such instability.

Oxygen-18 isotope effects in the liquid water–pyridine system as a probe of intermolecular forces

Oxygen-18 exchange between gaseous carbon dioxide and water in liquid water–pyridine mixtures is used as a probe for changes in intermolecular forces when the composition of the system is changed from pure water to pure pyridine. In agreement with results obtained previously by other methods, it is found that the interaction energy of an 'average' water molecule with the medium decreases when the mole fraction of pyridine is varied from zero to unity. The experimental results are related to the vapour pressure isotope effect, P(H218O)/P(H216O), of the binary mixtures. The utility of the Stern – Van Hook – Wolfsberg equation for vapour pressure isotope effects has been investigated. In addition, a plot of the equilibrium constant of the oxygen-18 exchange reaction vs. the mole fraction of pyridine presents no evidence of the formation of stoichiometric pyridine–water complexes.

Lattice vibrational spectra of five crystal modifications of thiourea

Lattice vibrational spectra of the five polymorphic phases of thiourea were measured. Polarized Raman measurements were made on an oriented single crystal which allowed an unambiguous assignment of the observed Raman active lattice modes to the irreducible representations of the factor group. I.r. measurements were made on polycrystalline material; hence only a tentative assignment of the modes could be made. The observed intensities and frequencies varied almost linearly with temperature. No discontinuities in the frequencies or intensities were observed at the phase transition temperatures. These results indicate; therefore, that no large changes in intermolecular forces or crystal structure occur during these transitions. Mixing of translational and librational rigid motions is indicated by the relative Raman intensities of the A 1 g vibrations. Because of this mixing, a description of these modes in terms of either translational or librational motions could not be made.

Far Infra-red Spectroscopy at High Pressures

PRESSURES sufficiently high to give significant distortion to crystal lattices or dense amorphous systems have been used in combination with spectroscopic observation for some years. The efforts of Drickamer et al.1 have been conspicuously successful in this field but their spectroscopy has been in the ultra-violet, visible and near infra-red regions where the primary transitions are electronic. We have developed a new technique in which very high pressures are combined with far infra-red spectroscopy where absorption by lattice modes dominates, providing useful information about intermolecular interactions. Wilkinson and Sherman2 have made a beginning in this field by making studies on alkali halides used as the pressure transmitting media in Drickamer's techniques. However, in this article we describe methods which are of general purpose in the sense that the transmission of the system allows features at any far infra-red wavelength to be studied. The new technique is complementary to X-ray studies under pressure in that information can be obtained about the changes of intermolecular forces with changing lattice parameters and crystal structure.