Theoretical Prediction of Structures, Vibrational Circular Dichroism, and Infrared Spectra of Chiral Be4B8 Cluster at Different Temperatures.

Lowest-energy structures, the distribution of isomers, and their molecular properties depend significantly on geometry and temperature. Total energy computations using DFT methodology are typically carried out at a temperature of zero K; thereby, entropic contributions to the total energy are neglected, even though functional materials work at finite temperatures. In the present study, the probability of the occurrence of one particular Be4B8 isomer at temperature T is estimated by employing Gibbs free energy computed within the framework of quantum statistical mechanics and nanothermodynamics. To identify a list of all possible low-energy chiral and achiral structures, an exhaustive and efficient exploration of the potential/free energy surfaces is carried out using a multi-level multistep global genetic algorithm search coupled with DFT. In addition, we discuss the energetic ordering of structures computed at the DFT level against single-point energy calculations at the CCSD(T) level of theory. The total VCD/IR spectra as a function of temperature are computed using each isomer's probability of occurrence in a Boltzmann-weighted superposition of each isomer's spectrum. Additionally, we present chemical bonding analysis using the adaptive natural density partitioning method in the chiral putative global minimum. The transition state structures and the enantiomer-enantiomer and enantiomer-achiral activation energies as a function of temperature evidence that a change from an endergonic to an exergonic type of reaction occurs at a temperature of 739 K.

Effects of Temperature on Enantiomerization Energy and Distribution of Isomers in the Chiral Cu13 Cluster.

In this study, we report the lowest energy structure of bare Cu13 nanoclusters as a pair of enantiomers at room temperature. Moreover, we compute the enantiomerization energy for the interconversion from minus to plus structures in the chiral putative global minimum for temperatures ranging from 20 to 1300 K. Additionally, employing nanothermodynamics, we compute the probabilities of occurrence for each particular isomer as a function of temperature. To achieve that, we explore the free energy surface of the Cu13 cluster, employing a genetic algorithm coupled with density functional theory. Moreover, we discuss the energetic ordering of isomers computed with various density functionals. Based on the computed thermal population, our results show that the chiral putative global minimum strongly dominates at room temperature.

Chronic stress decreases ornithine decarboxylase expression and protects against 1,2-dimethylhydrazine-induced colon carcinogenesis.

Biological response to stress depends on the type, timing, and severity of the stressor. Acute stressful environments may positively activate molecular and cellular mechanisms to favor adaptation; however, chronic stress is often associated with detrimental health effects. Colon cancer (CC) is one of the leading causes of death associated with cancer and has been mentioned as a stress-related disease. In the present work, the effect of chronic stress on the initial phase of CC was evaluated, and special emphasis was placed on ornithine decarboxylase (ODC) expression and polyamines for their role in hyperproliferative diseases. BALB/c mice (n = 5/group) were administered the pro-carcinogen 1,2-dimethylhydrazine (DMH) for 8 weeks (20 mg/kg body weight/week) to induce colon carcinogenesis, and then exposed for 4 weeks to two physical stressors: restraint and forced-swimming. Distal colon inflammatory lesions and histomorphological changes were evaluated by hematoxylin-eosin staining; plasma corticosterone levels, colon ODC expression, and urinary polyamines were determined by competitive ELISA, RT-qPCR, Western Blot, and HPLC, respectively. The short-term exposure to DMH triggered colon inflammation, initiated colon carcinogenesis and increased ODC expression; meanwhile, the exposure to chronic stress activated the hypothalamic-pituitary-adrenal (HPA) axis, elicited the production of plasmatic corticosterone, and decreased ODC expression. The exposure of DMH-treated mice to chronic stress counteracted the inflammatory effect of DMH and maintained ODC homeostasis. In early phase of carcinogenesis, the exposure of DMH-treated mice to chronic stress had a positive effect against colon inflammation and maintained ODC homeostasis. The cross-talk between corticosterone, ODC expression, and inflammation in a tumor environment is discussed.

The Role of Nitrogen-Rich Moieties in the Selection of Arginine's Tautomeric Form at Different Temperatures.

It is well known that the guanidinium group in Arginine plays an important role in noncovalent interactions. However, its role is not well documented since the selection of its global minimum structure is still controversial. The main difficulties on obtaining accurate results lie on:  neutral Arginine can occur in 3 forms, two of which are canonical and one is zwitterion; each form has degenerate enantiomers D- and L-; its numerous degrees of freedom make it challenging to perform a thorough study; the short-range interactions require higher levels of theory to correctly describe them. Thus, we have performed a meticulous global minimum search. We performed optimizations of the systems at the PBE0 /Def2TZVP level of theory and single point calculations at the DLPNO-CCSD(T)/Def2TZVP level with zero-point corrections at PBE0 /Def2TZVP. We also analyzed Thermal Populations and IR Spectra of the systems to fully understand Arginine's behavior. The results show the energy minima structures strongly rely on its internal nitrogen-rich groups.

Relative Populations and IR Spectra of Cu38 Cluster at Finite Temperature Based on DFT and Statistical Thermodynamics Calculations.

The relative populations of Cu38 isomers depend to a great extent on the temperature. Density functional theory and nanothermodynamics can be combined to compute the geometrical optimization of isomers and their spectroscopic properties in an approximate manner. In this article, we investigate entropy-driven isomer distributions of Cu38 clusters and the effect of temperature on their IR spectra. An extensive, systematic global search is performed on the potential and free energy surfaces of Cu38 using a two-stage strategy to identify the lowest-energy structure and its low-energy neighbors. The effects of temperature on the populations and IR spectra are considered via Boltzmann factors. The computed IR spectrum of each isomer is multiplied by its corresponding Boltzmann weight at finite temperature. Then, they are summed together to produce a final temperature-dependent, Boltzmann-weighted spectrum. Our results show that the disordered structure dominates at high temperatures and the overall Boltzmann-weighted spectrum is composed of a mixture of spectra from several individual isomers.

Exploration of Free Energy Surface and Thermal Effects on Relative Population and Infrared Spectrum of the Be6B11- Flux-Ional Cluster.

The starting point to understanding cluster properties is the putative global minimum and all the nearby local energy minima; however, locating them is computationally expensive and difficult. The relative populations and spectroscopic properties that are a function of temperature can be approximately computed by employing statistical thermodynamics. Here, we investigate entropy-driven isomers distribution on Be6B11- clusters and the effect of temperature on their infrared spectroscopy and relative populations. We identify the vibration modes possessed by the cluster that significantly contribute to the zero-point energy. A couple of steps are considered for computing the temperature-dependent relative population: First, using a genetic algorithm coupled to density functional theory, we performed an extensive and systematic exploration of the potential/free energy surface of Be6B11- clusters to locate the putative global minimum and elucidate the low-energy structures. Second, the relative populations' temperature effects are determined by considering the thermodynamic properties and Boltzmann factors. The temperature-dependent relative populations show that the entropies and temperature are essential for determining the global minimum. We compute the temperature-dependent total infrared spectra employing the Boltzmann factor weighted sums of each isomer's infrared spectrum and find that at finite temperature, the total infrared spectrum is composed of an admixture of infrared spectra that corresponds to the spectra of the lowest-energy structure and its isomers located at higher energies. The methodology and results describe the thermal effects in the relative population and the infrared spectra.