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.

Mechanism of wettability alteration of the calcite {101[combining macron]4} surface.

To understand the mechanism of wettability alteration of calcite, a typical mineral in oil reservoirs, the interactions of deionized water and brine (with different compositions) with the calcite {101[combining macron]4} surface are investigated using a combination of molecular dynamics and first-principles simulations. We show that two distinct water adsorption layers are formed through hydrogen bonding and electrostatic interactions with the calcite {101[combining macron]4} surface as well as hydrogen bonding between the water molecules. These highly ordered water layers resist penetration of large stable Mg2+ and Ca2+ hydrates. As Na+ and Cl- hydrates are less stable, Na+ and Cl- ions may penetrate the ordered water layers to interact with the calcite {101[combining macron]4} surface. In contact with this surface, Na+ interacts significantly with water molecules, which increases the water-calcite interaction (wettability of calcite), in contrast to Cl-. We propose that formation of Na+ hydrates plays an important role in the wettability alteration of the calcite {101[combining macron]4} surface.

Detecting Hachimoji DNA: An Eight-Building-Block Genetic System with MoS2 and Janus MoSSe Monolayers.

In the pursuit of personalized medicine, the development of efficient, cost-effective, and reliable DNA sequencing technology is crucial. Nanotechnology, particularly the exploration of two-dimensional materials, has opened different avenues for DNA nucleobase detection, owing to their impressive surface-to-volume ratio. This study employs density functional theory with van der Waals corrections to methodically scrutinize the adsorption behavior and electronic band structure properties of a DNA system composed of eight hachimoji nucleotide letters adsorbed on both MoS2 and MoSSe monolayers. Through a comprehensive conformational search, we pinpoint the most favorable adsorption sites, quantifying their adsorption energies and charge transfer properties. The analysis of electronic band structure unveils the emergence of flat bands in close proximity to the Fermi level post-adsorption, a departure from the pristine MoS2 and MoSSe monolayers. Furthermore, leveraging the nonequilibrium Green's function approach, we compute the current-voltage characteristics, providing valuable insights into the electronic transport properties of the system. All hachimoji bases exhibit physisorption with a horizontal orientation on both monolayers. Notably, base G demonstrates high sensitivity on both substrates. The obtained current-voltage (I-V) characteristics, both without and with base adsorption on MoS2 and the Se side of MoSSe, affirm excellent sensing performance. This research significantly advances our understanding of potential DNA sensing platforms and their electronic characteristics, thereby propelling the endeavor for personalized medicine through enhanced DNA sequencing technologies.

On the role of Hoogsteen:Hoogsteen interactions in RNA: ab initio investigations of structures and energies.

We use a combination of database analysis and quantum chemical studies to investigate the role of cis and trans Hoogsteen:Hoogsteen (H:H) base pairs and associated higher-order structures in RNA. We add three new examples to the list of previously identified base-pair combinations belonging to these families and, in addition to contextual classification and characterization of their structural and energetic features, we compare their interbase interaction energies and propensities toward participation in triplets and quartets. We find that some base pairs, which are nonplanar in their isolated minimum energy geometries, attain planarity and stability upon triplet formation. A:A H:H trans is the most frequent H:H combination in RNA structures. This base pair occurs at many distinct positions in known rRNA structures, where it helps in the interaction of ribosomal domains in the 50S subunit. It is also present as a part of tertiary interaction in tRNA structures. Although quantum chemical studies suggest an intrinsically nonplanar geometry for this base pair in isolated form, it has the tendency to attain planar geometry in RNA crystal structures by forming higher-order tertiary interactions or in the presence of additional base-phosphate interactions. The tendency of this base pair to form such additional interactions may be helpful in bringing together different segments of RNA, thus making it suitable for the role of facilitator for RNA folding. This also explains the high occurrence frequency of this base pair among all H:H interactions.

Genetic algorithm optimization of laser pulses for molecular quantum state excitation.

Conventionally optimal control theory has been used in the theoretical design of laser pulses through the direct variation in the electric field of the laser pulse as a function of time. This often leads to designed laser pulses which contain a broad and seemingly arbitrary frequency structure that varies in time in a manner which may be difficult to realize experimentally. In contrast, the experimental design of laser pulses has used a genetic algorithm (GA) approach, varying only those laser parameters actually available to the experimentalist. We investigate in this paper the possibility of using GA optimization methods in the theoretical design of laser pulses to bring about quantum state transitions in molecules. This allows us to select only a small limited number of parameters to vary and to choose these parameters so that they correspond to those available to the experimentalist. In the paper we apply our methods to the vibrational-rotational excitation of the HF molecule. We choose a small limited number of frequencies and vary only the associated electric field amplitudes and pulse envelopes. We show that laser pulses designed in this way can lead to very high transition probabilities.

Design of an infrared laser pulse to control the multiphoton dissociation of the Fe-CO bond in CO-heme compounds.

Optimal control theory is used to design a laser pulse for the multiphoton dissociation of the Fe-CO bond in the CO-heme compounds. The study uses a hexacoordinated iron-porphyrin-imidazole-CO complex in its ground electronic state as a model for CO liganded to the heme group. The potential energy and dipole moment surfaces for the interaction of the CO ligand with the heme group are calculated using density functional theory. Optimal control theory, combined with a time-dependent quantum dynamical treatment of the laser-molecule interaction, is then used to design a laser pulse capable of efficiently dissociating the CO-heme complex model. The genetic algorithm method is used within the mathematical framework of optimal control theory to perform the optimization process. This method provides good control over the parameters of the laser pulse, allowing optimized pulses with simple time and frequency structures to be designed. The dependence of photodissociation yield on the choice of initial vibrational state and of initial laser field parameters is also investigated. The current work uses a reduced dimensionality model in which only the Fe-C and C-O stretching coordinates are explicitly taken into account in the time-dependent quantum dynamical calculations. The limitations arising from this are discussed in Sec. IV.

Flexible C6BN Monolayers As Promising Anode Materials for High-Performance K-Ion Batteries.

K-ion batteries attract extensive attention and research efforts because of the high energy density, low cost, and high abundance of K. Although they are considered suitable alternatives to Li-ion batteries, the absence of high-performance electrode materials is a major obstacle to implementation. On the basis of density functional theory, we systematically study the feasibility of a recently synthesized C6BN monolayer as anode material for K-ion batteries. The specific capacity is calculated to be 553 mAh/g (K2C6BN), i.e., about twice that of graphite. The C6BN monolayer is characterized by high strength (in-plane stiffness of 309 N/m), excellent flexibility (bending strength of 1.30 eV), low output voltage (average open circuit voltage of 0.16 V), and excellent rate performance (diffusion barrier of 0.09 eV). We also propose two new C6BN monolayers. One has a slightly higher total energy (0.10 eV) than the synthesized C6BN monolayer, exhibiting enhanced electronic properties and affinity to K. The other is even energetically favorable due to B-N bonding. All three C6BN monolayers show good dynamical, thermal, and mechanical stabilities. We demonstrate excellent cyclability and improved conductivity by K adsorption, suggesting great potential in flexible energy-storage devices.

Selective Toluene Detection with Mo2CTx MXene at Room Temperature.

MXenes are a promising class of two-dimensional materials with several potential applications, including energy storage, catalysis, electromagnetic interference shielding, transparent electronics, and sensors. Here, we report a novel Mo2CTx MXene sensor for the successful detection of volatile organic compounds (VOCs). The proposed sensor is a chemiresistive device fabricated on a Si/SiO2 substrate using photolithography. The impact of various MXene process conditions on the performance of the sensor is evaluated. The VOCs, such as toluene, benzene, ethanol, methanol, and acetone, are studied at room temperature with varying concentrations. Under optimized conditions, the sensor demonstrates a detection limit of 220 ppb and a sensitivity of 0.0366 Ω/ppm at a toluene concentration of 140 ppm. It exhibits an excellent selectivity toward toluene against the other VOCs. Ab initio simulations demonstrate selectivity toward toluene in line with the experimental results.

A theoretical study on interaction of small gold clusters Au(n) (n = 4, 6, 8) with xDNA base pairs.

xDNA constitutes a novel class of size expanded synthetic nucleic acids in which one of the bases of the base pairs is larger than the natural DNA bases. These expanded bases are called x-bases. In this paper, we investigate the hydrogen bonding characteristics and relevant molecular properties of model complexes (xA...T)-Au(n), (xT...A)-Au(n), (xG...C)-Au(n), and (xC...G)-Au(n) (n = 4, 6, 8) consisting of xDNA base pairs and gold clusters, in order to study the nature of gold-xDNA binding. We offer detailed characterization of their different aspects, viz., structural, electronic and spectroscopic, effect of gold cluster size, aromaticity, and planarity using quantum mechanics based density functional theory (DFT). Significant charge transfer is seen between the gold clusters and x-base pairs. Gold complexation is found to affect the interbase hydrogen bonding in these complexes. In addition to anchor bonds, X-H...Au type of hydrogen bonding interactions are also found to contribute to the gold-base pair binding in these complexes.

Quantum chemical studies of structures and binding in noncanonical RNA base pairs: the trans Watson-Crick:Watson-Crick family.

The trans Watson-Crick/Watson-Crick family of base pairs represent a geometric class that play important structural and possible functional roles in the ribosome, tRNA, and other functional RNA molecules. They nucleate base triplets and quartets, participate as loop closing terminal base pairs in hair pin motifs and are also responsible for several tertiary interactions that enable sequentially distant regions to interact with each other in RNA molecules. Eleven representative examples spanning nine systems belonging to this geometric family of RNA base pairs, having widely different occurrence statistics in the PDB database, were studied at the HF/6-31G (d, p) level using Morokuma decomposition, Atoms in Molecules as well as Natural Bond Orbital methods in the optimized gas phase geometries and in their crystal structure geometries, respectively. The BSSE and deformation energy corrected interaction energy values for the optimized geometries are compared with the corresponding values in the crystal geometries of the base pairs. For non protonated base pairs in their optimized geometry, these values ranged from -8.19 kcal/mol to -21.84 kcal/mol and compared favorably with those of canonical base pairs. The interaction energies of these base pairs, in their respective crystal geometries, were, however, lesser to varying extents and in one case, that of A:A W:W trans, it was actually found to be positive. The variation in RMSD between the two geometries was also large and ranged from 0.32-2.19 A. Our analysis shows that the hydrogen bonding characteristics and interaction energies obtained, correlated with the nature and type of hydrogen bonds between base pairs; but the occurrence frequencies, interaction energies, and geometric variabilities were conspicuous by the absence of any apparent correlation. Instead, the nature of local interaction energy hyperspace of different base pairs as inferred from the degree of their respective geometric variability could be correlated with the identities of free and bound hydrogen bond donor/acceptor groups present in interacting bases in conjunction with their tertiary and neighboring group interaction potentials in the global context. It also suggests that the concept of isostericity alone may not always determine covariation potentials for base pairs, particularly for those which may be important for RNA dynamics. These considerations are more important than the absolute values of the interaction energies in their respective optimized geometries in rationalizing their occurrences in functional RNAs. They highlight the importance of revising some of the existing DNA based structure analysis approaches and may have significant implications for RNA structure and dynamics, especially in the context of structure prediction algorithms.

Interactions of atrazine with transition metal ions in aqueous media: experimental and computational approach.

Transition metal ions have their own significances and utility. Externally applied pesticides may alter the bioavailability of these metal ions to plants through the coordinating ability of these pesticides with metal ions. In current study a series of metal complexes containing atrazine (Atr) group(s) attached to metal(II) (M) frame, with the formula; [M(Atr)n.xH2O.yCl] (where M = Mn, Fe, Co, Ni, Cu or Zn; n = 1 or 2; x = 1-4; y = 1-2), have been synthesized for the first time to check the interactions of atrazine with transition metal ions. More importantly, all the complexes were synthesized at neutral pH in aqueous medium. The major differences among the FTIR spectra were observed between 3,700-2,800 and 1,800-1,350 cm-1. On the basis of FTIR, CHN and computational study, it was observed that Mn, Ni and Cu formed complexes in 1:2 and Fe, Co and Zn in 1:1. The obtained results were supported by 3D molecular modeling using GAMESS computations as a package of ChemBio3D Ultra14 program. The FTIR spectral analysis and 3D molecular modeling suggests that the Atr can show coordination through the nitrogen (in between two side chains) of ring as well as nitrogen (non steric amine) of side chain with different metal ions.

On the role of the cis Hoogsteen:sugar-edge family of base pairs in platforms and triplets-quantum chemical insights into RNA structural biology.

Base pairs belonging to the cis Hoogsteen:sugar-edge (H:S) family play important structural roles in folded RNA molecules. Several of these are present in internal loops, where they are involved in interactions leading to planar dinucleotide platforms which stabilize higher order structures such as base triplets and quartets. We report results of analysis of 30 representative examples spanning 16 possible base pair combinations, with several of them showing multimodality of base pairing geometry. The geometries of 23 of these base pairs were modeled directly from coordinates extracted from RNA crystal structures. The other seven were predicted structures which were modeled on the basis of observed isosteric analogues. After appropriate satisfaction of residual valencies, these structures were relaxed using the B3LYP/6-31G(d,p) method and interaction energies were derived at the RIMP2/aug-cc-pVDZ level of theory. The geometries for each of the studied base pairs have been characterized in terms of the number and nature of H-bonds, rmsd values observed on optimization, base pair geometrical parameters, and sugar pucker analysis. In addition to its evaluation, the nature of intermolecular interaction in these complexes was also analyzed using Morokuma decomposition. The gas phase interaction energies range between -5.2 and -20.6 kcal/mol and, in contrast to the H:S trans base pairs, show enhanced relative importance of the electron correlation component, indicative of the greater role of dispersion energy in stabilization of these base pairs. The rich variety of hydrogen bonding pattern, involving the flexible sugar edge, appears to hold the key to several features of structural motifs, such as planarity and propensity to participate in triplets, observed in this family of base pairs. This work explores these aspects by integrating database analysis, and detailed base pairing geometry analysis at the atomistic level, with ab initio computation of interaction energies. The study, involving alternative classification of base pairs and triplets, provides insights into intrinsic properties of these base pairs and their possible structural and functional roles.

Modeling the noncovalent interactions at the metabolite binding site in purine riboswitches.

We present gas phase quantum chemical studies on the metabolite binding interactions in two important purine riboswitches, the adenine and guanine riboswitches, at the B3LYP/6-31G(d,p) level of theory. In order to gain insights into the strucutral basis of their discriminative abilities of regulating gene expression, the structural properties and binding energies for the gas phase optimized geometries of the metabolite bound binding pocket are analyzed and compared with their respective crystal geometries. Kitaura-Morokuma analysis has been carried out to calculate and decompose the interaction energy into various components. NBO and AIM analysis has been carried out to understand the strength and nature of binding of the individual aptamer bases with their respective purine metabolites. The Y74 base, U in case of adenine riboswitch and C in case of guanine riboswitch constitutes the only differentiating element between the two binding pockets. As expected, with W:W cis G:C74 interaction contributing more than 50% of the total binding energy, the interaction energy for metabolite binding as calculated for guanine (-46.43 Kcal/mol) is nearly double compared to the corresponding value for that of adenine (-24.73 Kcal/mol) in the crystal context. Variations in the optimized geometries for different models and comparison of relative contribution to metabolite binding involving four conserved bases reveal the possible role of U47:U51 W:H trans pair in the conformational transition of the riboswitch from the metabolite free to metabolite bound state. Our results are also indicative of significant contributions from stacking and magnesium ion interactions toward cooperativity effects in metabolite recognition.

Design of laser pulses for selective vibrational excitation of the N6-H bond of adenine and adenine-thymine base pair using optimal control theory.

Time dependent quantum dynamics and optimal control theory are used for selective vibrational excitation of the N6-H (amino N-H) bond in free adenine and in the adenine-thymine (A-T) base pair. For the N6-H bond in free adenine we have used a one dimensional model while for the hydrogen bond, N6-H(A)...O4(T), present in the A-T base pair, a two mathematical dimensional model is employed. The conjugate gradient method is used for the optimization of the field dependent cost functional. Optimal laser fields are obtained for selective population transfer in both the model systems, which give virtually 100% excitation probability to preselected vibrational levels. The effect of the optimized laser field on the other hydrogen bond, N1(A)...H-N3(T), present in A-T base pair is also investigated.

Binding of Gold Nanoclusters with Size-Expanded DNA Bases: A Computational Study of Structural and Electronic Properties.

Binding of gold nanoclusters with size-expanded DNA bases, xA, xC, xG, and xT, is studied using quantum chemical methods. Geometries of the neutral xA-Au6, xC-Au6, xG-Au6, and xT-Au6 complexes were fully optimized using the B3LYP density functional method (DFT). The gold clusters around xA and xT adopt triangular geometries, whereas irregular structures are obtained in the case of gold clusters complexed around xC and xG. The lengths of the bonds between atoms in the x-bases increase on gold complexation. The aromatic character of the x-bases also increases on gold complexation except for the five-member rings. A significant charge transfer from the x-base to gold atoms is seen in these complexes. Second-order interactions are observed in addition to direct covalent bonds between gold atoms and x-bases.