Sulfur Centered Hydrogen Bonding in Thioglycolic Acid and Its Clusters: A Computational Exploration.

The conformational landscape of thioglycolic acid (TGA) was investigated by using the CCSD/cc-pVTZ level of theory. The GGC conformer was identified as the global minimum, followed by the GAC conformer. The calculated rotational constant for the GGC conformer exhibited good agreement with the previously reported experimental results. Subsequently, the study delved into the exploration of sulfur-centered hydrogen bonding in TGA's dimer and trimer clusters, employing the CCSD/cc-pVDZ level of theory. These clusters revealed the participation of both oxygen and sulfur atoms in noncovalent H-bonding, contributing to their stability. The presence of these noncovalent interactions in TGA clusters was elucidated through Atoms in Molecule (AIM), reduced density gradient (RDG), and natural bond order (NBO) analysis, while electrostatic potential (ESP) charge and vibrational mode analysis further supported these findings.

To dimerize or not: para-aminothiophenol on a bismuth heterostructure.

Surface enhanced Raman spectroscopy (SERS) of p-aminothiophenol (PATP) was investigated on ß-Bi2O3/Bi2O2CO3 nanoparticles, a novel bismuth based metal substrate with the lowest limit of detection of 1 mM. Unlike on noble metal surfaces where PATP gets converted to p,p'-dimercaptoazobenzene (DMAB) due to photocatalytic coupling, no such transformation of PATP was observed on ß-Bi2O3/Bi2O2CO3 nanoparticles. Density functional theory (DFT) calculations at the PW91PW91/LANL2DZ/6-311+G(d,p) level of theory supported the experimental results exceedingly well. Also, the charge transfer direction from PATP to ß-Bi2O3/Bi2O2CO3 nanoparticles was revealed by the projected density of states calculation.

Predicting odor from molecular structure: a multi-label classification approach.

Decoding the factors behind odor perception has long been a challenge in the field of human neuroscience, olfactory research, perfumery, psychology, biology and chemistry. The new wave of data-driven and machine learning approaches to predicting molecular properties are a growing area of research interest and provide for significant improvement over conventional statistical methods. We look at these approaches in the context of predicting molecular odor, specifically focusing on multi-label classification strategies employed for the same. Namely binary relevance, classifier chains, and random forests adapted to deal with such a task. This challenge, termed quantitative structure-odor relationship, remains an unsolved task in the field of sensory perception in machine learning, and we hope to emulate the results achieved in the field of vision and auditory perception in olfaction over time.

Improved Estimates of Host-Guest Interaction Energies for Endohedral Fullerenes Containing Rare Gas Atoms, Small Molecules, and Cations.

Endohedral fullerenes have evinced much interest from the fundamental and applications points of view. However, given the nature of the weak interaction between the guest species and the host cage in these confined systems, the interaction energy values obtained using various theoretical methods, and different basis sets vary over a wide range. For example, the reported interaction energy for the HF@C60 system ranges from -2.5 kcal/mol to -14.9 kcal/mol. In the present manuscript, we report reliable interaction energy values for different endohedral fullerenes (He@C60 , Ne@C60 , Ar@C60 , Kr@C60 , H2 @C60 , HF@C60 , H2 O@C60 , NH3 @C60 , CH4 @C60 , Li+ @C60 , Na+ @C60 , and K+ @C60 ) obtained using the domain-based local pair natural orbital coupled-cluster singles, doubles, and perturbative triples (DLPNO-CCSD(T)) method and the def2-TZVP basis set. We believe that these energy values could be considered as benchmark values, and the performance of other quantum chemical methods could be assessed accordingly. Local energy decomposition analysis within the DLPNO-CCSD(T) framework is used to estimate the electrostatic, exchange, and dispersion components of the interaction energy for some of the endohedral fullerenes.

Bismuth based novel substrate for surface enhanced Raman spectroscopy.

Exploring the potential of non-noble metal substrates for Surface-enhanced Raman spectroscopy (SERS) has attracted considerable interest in recent years. In this work, we prepared nanoplate ß-Bi2O3/Bi2O2CO3 heterostructure via calcination of Bi2O2CO3 precursor using a facile hydrothermal process and successfully demonstrated its use as a novel SERS substrate. The SERS sensitivity of substrate was performed by probing methyl orange (MO), rhodamine B (RhB), vitamin C (Vit. C), and melamine. The observed results show that the SERS signal is enhanced considerably by the adsorption of probe molecules on the surface of the Bismuth heterostructure SERS substrate.

Conformational and structural stability of n and 2-propylthiols: a revisit.

The conformational and structural stability of n-propanethiol (nP) is revisited owing to the prevailing ambiguity in the literature reported hitherto, and the rationale for 2-propanethiol's (2P) most stable conformers is analyzed. Based on the rotation around the C-C and C-S bonds, four conformers for nP and two conformers for 2-propanethiol (2P) were found to have the lowest energies at the CCSD/cc-pVDZ level of theory. The two conformers of 2P are anti (T), and gauche (G), and those of nP are T-G, G-G, T-T, and G-T. Rotational barriers, geometrical parameters, fundamental vibrational modes, and energy parameters reported herein agree exceedingly well with the reported experimental values for nP and 2P molecules. Furthermore, natural bond orbital (NBO), frontier molecular orbital (FMO), Mulliken charge (MC), electrostatic potential charge (ESP), and vibrational mode analyses were carried out to get a better understanding of both the thiols.

Conformational stability and structural analysis of methanethiol clusters: a revisit.

B3LYP/cc-pV(D/T/Q)Z and CCSD/cc-pVDZ levels of theory predict three minima for both dimers and trimers of methanethiol. Predictions at B3LYP/cc-pVDZ corroborates exceedingly well with the earlier reported experimental value but significantly differ from the previous computational predictions. Interaction energy between the molecules decreases with an increase in the size of the basis set for both the dimer and trimer. The dipole moment of methanethiol dimer gets reduced at the B3LYP/cc-pVDZ level of theory relative to all minima configurations, and the same is seen for trimer also. These new predictions are well supported by atoms in molecules (AIM), frontier molecular orbital (FMO), Mulliken charge (MC), and natural bond orbital (NBO) analysis.

Lone pair ... pi interactions between water oxygens and aromatic residues: quantum chemical studies based on high-resolution protein structures and model compounds.

The pi electron cloud of aromatic centers is known to be involved in several noncovalent interactions such as C--H...pi, O--H...pi, and pi...pi interactions in biomolecules. Lone-pair (lp) ... pi interactions have gained attention recently and their role in biomolecular structures is being recognized. In this article, we have carried out systematic analysis of high-resolution protein structures and identified more than 400 examples in which water oxygen atoms are in close contact (distance < 3.5 A) with the aromatic centers of aromatic residues. Three different methods were used to build hydrogen atoms and we used a consensus approach to find out potential candidates for lp...pi interactions between water oxygen and aromatic residues. Quantum mechanical calculations at MP2/6-311++G(d,p) level on model systems based on protein structures indicate that majority of the identified examples have energetically favorable interactions. The influence of water hydrogen atoms was investigated by sampling water orientations as a function of two parameters: distance from the aromatic center and the angle between the aromatic plane and the plane formed by the three water atoms. Intermolecular potential surfaces were constructed using six model compounds representing the four aromatic amino acids and 510 different water orientations for each model compound. Ab initio molecular orbital calculations at MP2/6-311++G(d,p) level show that the interaction energy is favorable even when hydrogen atoms are farthest from the aromatic plane while water oxygen is pointing toward the aromatic center. The strength of such interaction depends upon the distance of water hydrogen atoms from the aromatic substituents. Our calculations clearly show that the lp...pi interactions due to the close approach of water oxygen and aromatic center are influenced by the positions of water hydrogen atoms and the aromatic substituents.