Mg-Containing Zn3O3 Structures for Detection of CO2: A DFT Study on CHEM Effects of SERS and Electronic Properties.

Surface-enhanced Raman spectra (SERS) and electronic-structure-based properties are important tools for investigation of the molecular sensing ability of nanoparticles. The present computational study is intended to explore the sensing ability of Zn3O3 and Mg-containing Zn3O3 structures for CO2 molecules by CHEM effects of the SERS technique. Geometries of CO2-adsorbed Zn3O3, Zn2MgO3 (Mg as a substitutional impurity), and Zn3O3Mg (Mg as an interstitial impurity) structures are modeled using the B3LYP/6-31G(d,p) level of density functional theory. The Mg site of the Zn2MgO3 and Zn3O3Mg structures is preferential for the adsorption of CO2. The observed energy trends are supported by geometrical analysis, molecular orbital interactions, redshifts in CO2 vibrational modes, and topological properties. Raman activity enhancement of the CO2 symmetric vibrational mode is significant when the molecule is adsorbed at the Mg site of Zn3O3Mg. The observed Raman activity enhancement is supported by SERS spectra obtained from anharmonic calculations carried out on B3LYP/6-31G(d,p) geometries and substantiated by a larger change in the polarizability with energy corresponding to the symmetric vibrational mode of CO2. The TDDFT calculations, frequency-dependent polarizabilities, and charge transfer interactions show that Zn3O3Mg is a good substrate for sensing of CO2, with visible wavelengths, by resonance Raman effect. The trends with adsorption energy, Raman activity, and excited state properties are also substantiated by B3LYP/6-311+G(d,p) calculations.

Influence of the Number, Nature and Position of Methyl Posttranscriptional Modifications on Nucleobase Stacking in RNA.

DFT calculations are employed to quantify the influence of the presence, number, nature, and position of posttranscriptional methylation on stacking strength of RNA bases. We carry out detailed potential energy scans of the variation in stacking energies with characteristic geometrical parameters in three categories of forty stacked dimers - canonical base homodimers (N||N), methylated base homodimers (mN||mN) and heterodimers of canonical bases and methylated counterparts (N||mN). Our analysis reveals that neutral methylation invariably enhances the stacking of bases. Further, N||mN stacking is stronger than mN||mN stacking and charged N||mN exhibit strongest stacking among all dimers. This indicates that methylations greatly enhance stacking when dispersed in RNA sequences containing identical bases. Comparison of stacks involving singly- and doubly-methylated purines reveal that incremental methylation enhances the stacking in neutral dimers. Although methylation at the carbon position of neutral pyrimidine dimers greatly enhances the stacking, methylation on the 5-membered ring imparts better stacking compared to methylation on the 6-membered ring in adenine dimers. However, methylation at the ring nitrogen (N1 ) provides better stacking than the amino group (N2 ) in guanine dimers. Our results thus highlight subtle structural effects of methylation on RNA base stacking and will enhance our understanding of the physicochemical principles of RNA structure and dynamics.

A DFT study on reaction force approach of ammonia catalysed amide bond formation reaction between ammonia and formic acid.

A reaction force approach of ammonia catalysed stepwise amide bond formation between ammonia and formic acid is investigated using B3LYP/6-31G (d,p) level of density functional theory in gas phase. The stepwise amide bond formation mechanism involves two transition states, namely, TS1, in initial stage and TS2, in final stage of reaction pathway. The potential energy surfaces obtained from IRC calculations on transition state geometries are subjected to reaction force and reaction work calculations. The estimated reaction works of structural and electronic activities in the progress of reaction reflect the unfavorable formation of diol intermediate and preferential formation of formamide. While 91% of the activation energy comes from structural changes in preparative region of TS1 path, the structural and electronic rearrangements respectively, share 57.6% and 42.4% of total activation energy of TS2 pathway. The atomic resolution of IRC pathways and natural charge analysis reveal the importance of hydrogen atom of catalyst in TS1 path and the oxygen of water molecule in TS2 path in the progress of reaction.

A DFT study on the role of long range correlation interaction and solvent effects in homochiral and heterochiral cyclic trimerization of imidazole based heterocyclic amino acids.

Using B3LYP and B97D functionals of density functional theory (DFT), homochiral and heterochiral cyclic trimerization of imidazole based heterocyclic amino acids are studied in gas phase and solvent phase, i. e., Acetonitrile. Both the functionals show that formation of homochiral cyclic tripeptide is thermodynamically and kinetically favorable over its heterochiral counterpart in gas phase. The functional, B97D, decreases the height of reaction barriers significantly compared to those predicted by the functional B3LYP. The reaction pathways explored using PCM implicit solvent model show reduced kinetic favorability for formation of the homochiral cyclic tripeptide over its heterochiral counterpart. The results are substantiated by structural aspects.

Inter- versus intra-molecular cyclization of tripeptides containing tetrahydrofuran amino acids: a density functional theory study on kinetic control.

Density functional B3LYP method was used to investigate the preference of intra- and inter-molecular cyclizations of linear tripeptides containing tetrahydrofuran amino acids. Two distinct model pathways were conceived for the cyclization reaction, and all possible transition states and intermediates were located. Analysis of the energetics indicate intermolecular cyclization being favored by both thermodynamic and kinetic control. Geometric and NBO analyses were performed to explain the trends obtained along both the reaction pathways. Conceptual density functional theory-based reactive indices also show that reaction pathways leading to intermolecular cyclization of the tripeptides are relatively more facile compared to intramolecular cyclization.