Basis Set Research Articles

Hyperhardness and hypersoftness of atoms and their ions

ContextThe theory of reactivity based on cDFT has been supplemented with the new method of calculating the atomic and local indices. With the use of previously derived relationship of the electron density gradient to the softness kernel and to the linear response function, we deliver theoretical analysis to obtain significant reactivity indices—the electron density derivatives: local softness and local hypersoftness together with the global hyperhardness index and the derivative of the global softness with respect to the number of electrons. The local derivatives have been applied in the calculation of responses of atoms to perturbation by an external potential by the alchemical approach. The vital role of the local softness has been confirmed; the potential role of the hypersoftness has been indicated.MethodOur original theoretical scheme has been numerically illustrated with the results obtained with electron density calculations with B3LYP method implemented in Gaussian 16 package. The aug-cc-pvqz basis set has been routinely applied, except for the Ca atom (cc-pvqz). Using the pVTZ basis set recommended by Sadlej was necessary for the potassium atom.Graphical

Density functional theory (DFT) study of water autoionization in solvated clusters.

We have implemented a cluster-continuum method using density functional theory to model water clusters and various charged species derived from water. The two aims of this study are to determine the minimal basis required for proper modeling of water autoionization and to determine the minimum number of explicit water molecules required to properly model the energetics of solvation. The thermodynamics of water autoionization converge following a modified power law to deliver chemically accurate values of the Gibbs energy change for autoionization with tractably small clusters. Convergence is slower and not exponential as assumed in previous work. We identify the n = 21 set of clusters as the first effectively bulk water like clusters that can capture the energetic influence of both the first and second solvation shells. In this cluster, a water molecule is encapsulated in the center of a closed shell of other water molecules that hydrogen bond to form five-membered rings. The total energy change for clusters with n ≥ 21 calculated using both the RPBE-D3 and ωB97X-D exchange-correlation functionals with the 6-311+G** basis set is shown to deliver good approximations to the free energy change at 298K. This is true even though neither functional models the individual enthalpy or entropy contributions particularly well.

Exploiting Non-Abelian Point-Group Symmetry to Estimate the Exact Ground-State Correlation Energy of Benzene in a Polarized Split-Valence Triple-Zeta Basis Set

Exploiting Non-Abelian Point-Group Symmetry to Estimate the Exact Ground-State Correlation Energy of Benzene in a Polarized Split-Valence Triple-Zeta Basis Set

Quantitative evaluation of noncovalent interactions with negative fragmentation approach including basis set superposition error correction

Abstract We propose a negative fragmentation approach (NFA), including counterpoise (CP) correction to basis set superposition error (BSSE) for quantitatively evaluating intra- and intermolecular noncovalent interactions. Noncovalent interactions are widely found in chemistry and biology and are regarded as essential interactions. However, there are few general methods for evaluating these individual intra- and intermolecular interaction energies because of two issues: (i) difficulty in the evaluation of intramolecular interactions due to the interacting sites connected with covalent bonds and (ii) BSSE affecting the quantitative accuracy of interaction analysis. In our scheme, we overcome the issue (i) using the NFA scheme, which can evaluate intra- and intermolecular interactions as a fragment–fragment interaction of interacting sites, and address the issue (ii) using the CP method. Here, NFA including the CP correction was applied to various molecular systems, providing comparable results for intermolecular interactions to supermolecule calculations with the CP correction and also succeeding in the evaluation of intramolecular interactions and its BSSEs. It is notable that our NFA scheme does not require any particular program or a modification of the program codes. These indicate that many researchers can apply our NFA scheme to various molecular systems.

Molecular Aspects of the Interactions between Selected Benzodiazepines and Common Adulterants/Diluents: Forensic Application of Theoretical Chemistry Methods

Benzodiazepines are frequently encountered in crime scenes, often mixed with adulterants and diluents, complicating their analysis. This study investigates the interactions between two benzodiazepines, lorazepam (LOR) and alprazolam (ALP), with common adulterants/diluents (paracetamol, caffeine, glucose, and lactose) using infrared (IR) spectroscopy and quantum chemical methods. The crystallographic structures of LOR and ALP were optimized using several functionals (B3LYP, B3LYP-D3BJ, B3PW91, CAM-B3LYP, M05-2X, and M06-2X) combined with the 6-311++G(d,p) basis set. M05-2X was the most accurate when comparing experimental and theoretical bond lengths and angles. Vibrational and 13C NMR spectra were calculated to validate the functional’s applicability. The differences between LOR’s experimental and theoretical IR spectra were attributed to intramolecular interactions between LOR monomers, examined through density functional theory (DFT) optimization and quantum theory of atoms in molecules (QTAIM) analysis. Molecular dynamics simulations modeled benzodiazepine–adulterant/diluent systems, predicting the most stable structures, which were further analyzed using QTAIM. The strongest interactions and their effects on IR spectra were identified. Comparisons between experimental and theoretical spectra confirmed spectral changes due to interactions. This study demonstrates the potential of quantum chemical methods in analyzing complex mixtures, elucidating spectral changes, and assessing the structural stability of benzodiazepines in forensic samples.

A Qubit-Efficient Variational Selected Configuration-Interaction Method

Abstract Finding the ground-state energy of molecules is an important and challenging computational problem for which quantum computing can potentially find efficient solutions. 
The variational quantum eigensolver (VQE) is a quantum algorithm that tackles the molecular groundstate problem and is regarded as 
one of the flagships of quantum computing. Yet, to date, 
only very small molecules were computed via VQE, due to high noise levels in current quantum devices. 
Here we present an alternative variational quantum scheme that requires significantly less qubits than VQE. 
The reduction in the qubit number allows for shallower circuits to be sufficient, rendering the method more resistant to noise.
The proposed algorithm, termed variational quantum selected-configuration-interaction (VQ-SCI), is based on:
(a) representing the target groundstate as a superposition of Slater determinant configurations, encoded directly upon the quantum computational basis states; and (b) selecting \emph{a-priory} only the most dominant configurations. 
This is demonstrated through a set of groundstate calculations of the H$_2$, LiH, BeH$_2$, H$_2$O, NH$_3$ and C$_2$H$_4$ molecules in the sto-3g basis set, performed on IBM quantum devices. We show that the VQ-SCI reaches the full configuration interaction (FCI) energy within chemical accuracy using the lowest number of qubits reported to date. 
Moreover, when the SCI matrix is generated ``on the fly", the VQ-SCI requires exponentially less memory than classical SCI methods. This offers a potential remedy to a severe memory bottleneck problem in classical SCI calculations. Finally, the proposed scheme is general and can be straightforwardly applied for finding the groundstate of any Hermitian matrix, outside the chemical context.

Optimization of damping function parameters for -D3 and -D4 dispersion models for Hartree-Fock based symmetry-adapted perturbation theory.

Symmetry-adapted perturbation theory (SAPT) directly computes intermolecular interaction energy in terms of electrostatics, exchange-repulsion, induction/polarization, and London dispersion components. In SAPT based on Hartree-Fock ("SAPT0") or based on density functional theory, the most time-consuming step is the computation of the dispersion terms. Previous work has explored the replacement of these expensive dispersion terms with simple damped asymptotic models. We recently examined [Schriber et al. J. Chem. Phys. 154, 234107 (2021)] the accuracy of SAPT0 when replacing its dispersion term with Grimme's popular -D3 correction, reducing the computational cost scaling from O(N5) to O(N3). That work optimized damping function parameters for SAPT0-D3/jun-cc-pVDZ using estimates of the coupled-cluster complete basis set limit [CCSD(T)/CBS] on a 8299 dimer dataset. Here, we explore the accuracy of SAPT0-D3 with additional basis sets, along with an analogous model using -D4. Damping parameters are rather insensitive to basis sets, and the resulting SAPT0-D models are more accurate on average for total interaction energies than SAPT0. Our results are surprising in several respects: (1) improvement of -D4 over -D3 is negligible for these systems, even charged systems where -D4 should, in principle, be more accurate; (2) addition of Axilrod-Teller-Muto terms for three-body dispersion does not improve error statistics for this test set; and (3) SAPT0-D is even more accurate on average for total interaction energies than the much more computationally costly density functional theory based SAPT [SAPT(DFT)] in an aug-cc-pVDZ basis. However, SAPT0 and SAPT0-D3/D4 interaction energies benefit from significant error cancellation between exchange and dispersion terms.

Cu(β-diketonato)2 bathochromic shifts from the ultraviolet towards the visible region

ContextThe DFT-calculated ultraviolet/visible properties of 11 different Cu(β-diketonato)2 complexes are presented. The selected β-diketonato ligands on the Cu complex contain none, one or two aromatic rings. The experimentally measured absorbance maxima range of the ultraviolet/visible is observed at 295–390 nm, and the calculated range is 302–425 nm, for the 11 complexes in this study. More aromatic rings on the ligand lead to bathochromic shifts of the experimentally measured absorbance maxima from the ultraviolet towards the visible region. Absorbance maxima of the Cu(β-diketonato)2 complexes with no aromatic rings on the ligand are found to be predominantly ligand-to-metal charge transfer excitations, whereas introducing one or two aromatic rings shifts the excitations to predominantly ligand-to-ligand charge transfer.MethodsDFT calculations were conducted on the neutral molecules with multiplicity 2, using the PBEh1PBE functional and the aug-cc-pVDZ basis set as implemented in the Gaussian 16 package. The selected solvent was acetonitrile, the solvent in which most of the experimental UV/Vis are reported. The molecules were all optimized in the solvent phase, using the IEFPCM. The initial coordinates for the compounds were generated using Chemcraft.HighlightsTDDFT of 11 different Cu(β-diketonato)2 complexes follow the experimental trend.Aromatic rings on the ligand lead to Bathochromic shifts of UV/Visible spectra.No aromatic rings on the ligand lead to ligand-to-metal charge transfer excitations.Aromatic rings on the ligand lead to ligand-to-ligand charge transfer excitations.Graphical abstractBathochromic shifts in eco-friendly Cu(β-diketonato)2.

Reconciling Accuracy and Feasibility for Barrierless Reaction Steps by the PCS/DDCI/MC-PDFT Protocol: Methane and Ethylene Dissociations as Case Studies.

Several enhancements have been introduced into state-of-the-art computational protocols for the treatment of barrierless reaction steps in the framework of variable reaction coordinate variational transition state theory. The first step is the synergistic integration of the Iterative Difference Dedicated Configuration Interaction (I-DDCI) and Pisa Composite Scheme, which defines a reduced cost, yet very accurate, computational workflow. This approach provides a near black box tool for obtaining 1D reference potentials. Then, a general strategy has been devised for tuning the level of theory used in Monte Carlo (MC) sampling, employing Multiconfiguration Pair Density Functional Theory (MC-PDFT) with dynamically adjusted Hartree-Fock exchange. Concurrently, partial geometry optimizations during the MC simulations account for the coupling between the reaction coordinates and conserved modes. The protocol closely approaches full size consistency and yields highly accurate results, with several test computations suggesting rapid convergence of the I-DDCI correction with the basis set dimensions. The capabilities of the new platform are illustrated by two case studies (the hydrogen dissociation from CH4 and C2H4), which highlight its flexibility in handling different carbon hybridizations (sp3 and sp2). The remarkable accuracy of the computed rate constants confirms the robustness of the proposed method. Together with their intrinsic interest, these results pave the way for systematic investigations of complex gas-phase reactions through a reliable, user-friendly tool accessible to specialists and nonspecialists alike.

Unraveling Strong Supramolecular Assembly of a Novel Pyrene Based Hg(II)‐complex: Insights from Hirshfeld Surface, FMO and Molecular Electrostatic Potential (MEP) Analyses

AbstractA rare pyrene‐based coordination compound of Hg(II) [Hg(L)2] (1) (where, HL=2‐((Pyren‐1‐ylmethylene)amino)benzenethiol) was synthesized and characterized by single crystal X‐ray diffraction (SC‐XRD) analysis. Crystallographic analysis revealed that complex 1 has seesaw geometry with HL coordinated as a bidentate ligand to a metal ion. The role of weak forces like π⋅⋅⋅π and CH⋅⋅⋅π interactions in influencing the self‐assembly process appears to be of importance. The electronic structure of the complex was predicted using DFT calculations with mixed basis set. DFT calculated structural parameters are in good agreement with the experimentally obtained parameters from XRD. Molecular reactivity and stability of the complex has been assessed through frontier molecular orbital analysis. Evaluation of molecular electrostatic potential (MEP) displays the electrophilic and nucleophilic reactivity sites. The Hirshfeld surface analysis clearly indicates C−H⋅⋅⋅π interactions and π⋅⋅⋅π stacking interactions are responsible to extend the supramolecular network of the complex. Analyses of the Finger print plots suggest that H⋅⋅⋅H and H⋅⋅⋅C contacts are major interactions for stabilizing the molecular crystal.

Enzyme Machinery for Bacterial Glucoside Metabolism through a Conserved Non-hydrolytic Pathway.

Flexible acquisition of substrates from nutrient pools is critical for microbes to prevail in competitive environments. To acquire glucose from diverse glycoside and disaccharide substrates, many free-living and symbiotic bacteria have developed, alongside hydrolysis, a non-hydrolytic pathway comprised of four biochemical steps and conferred from a single glycoside utilization gene locus (GUL). Mechanistically, this pathway integrates within the framework of oxidation and reduction at the glucosyl/glucose C3, the eliminative cleavage of the glycosidic bond and the addition of water in two consecutive lyase-catalyzed reactions. Here, based on study of enzymes from the phytopathogenAgrobacterium tumefaciens, we reveal a conserved Mn2+metallocenter active site in both lyases and identify the structural requirements for specific catalysis to elimination of 3-keto-glucosides and water addition to the resulting 2-hydroxy-3-keto-glycal product, yielding 3-keto-glucose. Extending our search of GUL-encoded putative lyases to the human gut commensalBacteroides thetaiotaomicron, we discover a Ca2+metallocenter active site in a putative glycoside hydrolase-like protein and demonstrate its catalytic function in the eliminative cleavage of 3-keto-glucosides of opposite (alpha) anomeric configuration as preferred by theA. tumefaciensenzyme (beta). Findings identify a basic set of GUL-encoded lyases for glucoside metabolism and assign physiological significance to GUL genetic diversity in bacteria.

Enzymmaschinerie für bakteriellen Glucosidmetabolismus über einen konservierten nicht‐hydrolytischen Abbauweg

AbstractFlexible Substrataufnahme aus Nährstoffreservoirs ist für Mikroorganismen entscheidend, um sich in kompetitiven natürlichen Umgebungen durchzusetzen. Zur Aufnahme von Glucose aus verschiedenen Glucosid‐ und Disaccharid‐Substraten haben viele frei‐ und symbiotisch lebende Bakterien, neben der Hydrolyse, einen nicht‐hydrolytischen Stoffwechselweg entwickelt. Dieser besteht aus vier biochemischen Schritten und wird von einem distinkten Genlocus (glycoside utilization locus, GUL) codiert. Mechanistisch integriert der Stoffwechselweg die Oxidation und Reduktion am Glucosyl/Glucose‐C3 mit der eliminativen Spaltung der glycosidischen Bindung und der Addition von Wasser an das Eliminationsprodukt in zwei aufeinanderfolgenden, von Lyasen katalysierten Reaktionen. In dieser Studie zeigen wir, basierend auf der Untersuchung von Enzymen des Pflanzenpathogens Agrobacterium tumefaciens, ein konserviertes Aktivitätszentrum in beiden Lyasen, welches um ein zentrales Mn2+ Metallion angeordnet ist. Weiters identifizieren wir die strukturellen Voraussetzungen für die spezifische Katalyse der 3‐Ketoglucosid Eliminierung zu 2‐Hydroxy‐3‐ketoglycal und der Hydratisierung des Glycal zu 3‐Ketoglucose. Die Erweiterung unserer Suche nach GUL‐codierten putativen Lyasen auf das menschliche darmkommensale Bakterium Bacteroides thetaiotaomicron führte uns zur Entdeckung eines Ca2+‐koordinierten Aktivitätszentrums in einem Glycosidase‐ähnlichen Protein. Das Enzym katalysiert die eliminative Spaltung von 3‐Ketoglucosiden entgegengesetzter (α) anomerer Konfiguration im Vergleich zu den von der A. tumefaciens Lyase präferierten Substraten (β). Strukturelle und biochemische Vergleiche zeigen die molekular‐mechanistische Basis der Stereokomplementarität der beiden 3‐Ketoglucosid Lyasen. Unsere Ergebnisse identifizieren ein grundlegendes Set von GUL‐codierten Lyasen für den Glucosidmetabolismus und erlauben es, der Gendiversität von GULs in der Domäne von Bakterien physiologische Bedeutung zuzuschreiben.

Synthesis, crystal structure, spectroscopic, electronic and vibrational properties of N′-[(E)-3-pyridinylmethylene]nicotinohydrazide trihydrate: Experimental and computational study

N′-[(E)-3-pyridinylmethylene]nicotinohydrazide trihydrate (C12H10N4O·3(H2O)) was synthesized and its structure was determined by single crystal X-ray diffraction method. X-ray analysis showed that the compound crystalized in the triclinic system P-1 with a = 7.1134 (3) Å, b = 10.0208 (4) Å, c = 10.3601 (4) Å, α = 96.386 (3)°, β = 96.995 (3)°, γ = 101.219 (4)°, V = 712.05 (5) Å3 and Z = 2 and exhibits that the title compound (I) consists of N′-[(E)-3-pyridinylmethylene]nicotinohydrazide (II) (C12H10N4O), and three water molecules of crystallization. The two water molecules are attached to the third water molecule through intermolecular two OH…O hydrogen bonds. At the same time, this water molecule is linked to the NH amide group of the hydrazone by an intermolecular NH…O hydrogen bond. Hirshfeld surface (HS) analyses were carried out are to visualise the intermolecular interactions in the crystals of Compound I. The geometric optimization of the titled compound has been carried out by different computational methods such as by Hatree Fock (HF) and Density Functional Theory (DFT) methods with the 6–311++G (d,p) basis set. The vibrational frequency, dipole moment (μ), polarizability (α), hyperpolarizability (β), and electronic properties including the highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO–LUMO) of the compound have been calculated at the level of both theories. In the results of crystal analysis and geometry calculations of the compound I, it was observed that intermolecular hydrogen bonds, N2H2A…O3, O3H31…O2 and O3H32…O4, were formed. The energy band gap (Eg = ELUMO-EHOMO) values were also obtained by using ELUMO and EHOMO at the level of both theories. The value of equilibrium (ground state) dipole moment of the studied molecule was calculated to be 8.31 Debye in B3LYP and 7.55 Debye in HF. The calculated hyperpolarizability values at the B3LYP/6–311++G(d,p) of the compound are 2.53 × 10−30 esu and this value corresponds to 6.79 times the hyperpolarizability value of urea.

The strongest dative bond in main-group compounds. Theoretical study of OAeF- (Ae = Be-Ba).

Quantum chemical calculations of the anions OAeF- (Ae = Be-Ba) have been carried out using ab initio methods at the CCSD(T)/def2-TZVPP level and density functional theory employing BP86 with various basis sets. The equilibrium structures have linear geometries for Ae = Be and Mg but they are strongly bent for Ae = Sr and Ba while the calcium species has a quasi-linear structure with a very low bending potential. The calculated bond dissociation energies suggest a record-high BDE of De = 144.08 kcal mol-1 for OBeF- at the CCSD(T)/def2-TZVPP level, which is the strongest BDE for a dative bond that has been found so far. The BDE of the heavier homologues have a continuously decreasing order for Ae with Be > Mg (113.01 kcal mol-1) > Ca (84.06 kcal mol-1) > Sr (72.06 kcal mol-1) > Ba (60.00 kcal mol-1). The calculation of the charge distribution reveals a significant charge donation OAe ← F- with a declining sequence for the heavier atoms Ae. The oxygen atom in OAeF- carries always a higher partial charge than the fluorine atom, which contradicts the standard electronegativities of the atoms. The surprising partial charges are explained with the bonding situation of the atoms in the actual electronic structure. The bonding analysis of the OAe-F- bonds using the EDA-NOCV method shows that the bonds have much more electrostatic character than the Ae-F- bonds in the diatomic anions. This finding is supported by the results of the LED partitioning approach. The dative interactions have three major and one minor component. The assignment of a quadruple bond for the heavier species with Ae = Ca, Sr, Ba is not reasonable. The driving force for the bent geometries is the accumulation of electronic charge in the lone-pair region at the Ae atoms, which enhances the electrostatic attraction with the other atoms. An adequate description of the bonding situation is given by the formula O--Ae+ ← F-.

Novel Cu(II) and Zn(II) Nanocomplexes Based on 5,6‐Diphenyl‐1,2,4‐Triazine: Preparation, Spectroscopic, TD‐DFT Calculations, Molecular Docking and Solvatochromic Studies

ABSTRACTThe reaction between 2‐hydroxy‐1‐naphthaldehyde and 3‐hydrazino‐5,6‐diphenyl‐1,2,4‐triazine produced a novel hydrazone ligand (DTHMN), which reacted with Cu(II) and Zn(II) metal ion in molar ratio 1:1, giving octahedral Cu(II)‐DTHMN and tetrahedral Zn(II)‐DTHMN nanosized complexes. The structural geometries have been elucidated on the basis of elemental analysis, nuclear magnetic resonance, infrared, electronic, and electron spin resonance spectra, and magnetic and molar conductance measurements as well as x‐ray diffraction and thermal analysis. TEM analysis showed that Zn(II)‐DTHMN complex has nano‐rode morphology shape. On the other hand, Cu(II)‐DTHMN has sphere shape within nanodomain. The DTHMN ligand exhibits ONN chelating sites through N‐triazine ring, azomethine nitrogen, and deprotonated OH group, forming the mononuclear metal complexes. The synthesized compounds showed a distinct solvatochromic behavior in different polar solvents. A bathochromic alteration is observed when moving from less to high polar solvents, indicating strong solute–solvent interactions accompanied by intramolecular charge transfer (ICT). The ground and excited state dipole moments of these compounds were determined experimentally by solvatochromic shift method using Bilot–Kawski, Lippert–Mataga, Bakhshiev, and Kawski–Chamma–Viallet functions and a microscopic Reichardt's solvent polarity parameter (ETN). The dipole moment is increased significantly upon excitation referring to stabilizing the excited species includes n–π* transition by polarity of solvent. The experimental results are generally consistent with those values obtained by B3LYP/GENECP method at 6‐311G(d,p) basis set for C, H, N, and O atoms and SDD (Stuttgart/Dresden) basis set for the metal atoms. The compounds were tested for antimicrobial efficiency against Gram‐positive bacteria, Gram‐negative bacteria, and fungus strain. Finally, molecular docking was used to study the interactions between donors (the current compounds) and receptors FabH–CoA complex (PDB code: 1HNJ).

Ab-initio Study of Structural, Spectroscopic and Electronic Properties of High Energy Explosive Molecules: DFT/TD-DFT Calculations

This research explores the ground state geometry and molecular properties of FOX-7 and nitroguanidine molecules, with a focus on their spectroscopic and electronic characteristics. Initially, the conformational space of each molecule was systematically scanned using molecular mechanic calculations and the most probable conformer structure was obtained for each molecule. Subsequently, geometry optimizations of molecules were conducted by using ab initio density functional theory (DFT) with Becke’s three-parameter hybrid-exchange functional, which combines the Lee–Yang–Parr correlation functional (B3LYP) method, and the standard 6-311++G(d,p) basis set. The theoretically determined geometrical parameters from optimized structure and experimental values available in the literature were compared, providing validation for the structural properties of both molecules. Furthermore, the stability and reactivity properties of both molecules are estimated in terms of HOMO-LUMO energies. Overall, this study contributes to a comprehensive understanding of the ground state geometry, molecular structure, and spectroscopic behavior of FOX-7 and nitroguanidine, paving the way for potential applications in various fields of science and technology.

Synthesis of novel thiazole derivatives containing 3-methylthiophene carbaldehyde as potent anti α-glucosidase agents: In vitro evaluation, molecular docking, dynamics, MM-GBSA, and DFT studies

Thiazole derivatives bearing thiophene carbaldehyde have been successfully prepared by refluxing 3-methylthiophene carbaldehyde with thiosemicarbazide in absolute ethanol followed by treating the obtained product with different phenacyl bromide to get thiazole products in better yields. These derivatives were confirmed using 1H-, 13C NMR, and EI-MS spectrometry techniques and finally subjected for their α-glucosidase inhibitory potential. Two compounds in the series including 2 g (IC50 = 9.00 ± 0.57 µM) and 2b (IC50 = 13.50 ± 0.20 µM) were found as the most potent α-glucosidase inhibitors better than the standard acarbose. Furthermore, the remaining five compounds attributed significantly to less activity. The studied molecules were calculated on the 6–31++g(d,p) basis set at B3LYP, HF, M062X levels with the help of the Gaussian package program, and their chemical activities were compared. Following that, the molecules' interactions with different α-glucosidase proteins (PDB IDs: 1R47 and 1UAS) were investigated, and their activities were contrasted. The binding free energy of the molecule with the best docking score is computed using MM/GBSA techniques. The comparative molecular dynamics simulations of the 2g-1UAS and 2g-1R47 complexes highlight the intricate balance of forces that govern biomolecular interactions. The findings suggest that while the 2g-1UAS complex forms more stable interactions, as indicated by lower RMSD values, the 2g-1R47 complex maintains its structural integrity through strong hydrogen bonds. Overall, the equilibrium conformations achieved by both complexes suggest they are well-suited for their roles in physiological environments.

Vibrational spectroscopic interpretation, solvent effect and molecular docking studies of TAAR1 partial agonist RO5263397

Density functional theory studies of TAAR1 (trace amine associated receptor 1) partial agonist RO5263397 carried out with precise and detailed spectroscopic investigation as well as validated experimentally. FT-IR, confocal Raman and UV–visible spectroscopic techniques were used to characterize the compound and corresponding theoretical calculations were carried out using DFT/B3LYP method with 6-311++G (d,p) basis set. Estimated and observed vibrational wavenumbers of the compound were assigned. UV–visible spectrum and FMOs (frontier molecular orbital) analysis reveals that the polarity affects the molecular reactivity and stability of the compound. Donor – acceptor interaction and second order perturbation energy have been explained using natural bond orbital analysis clarify the presence hydrogen bonds in the system. ELF and LOL studies visualises the localized and delocalized electrons in the title compound. RDG analysis evidences the various interactions present in the monomer and dimer of RO5263397. The structural importance of the compound were clearly examined using NMR spectral analysis. The existence of hydrogen bonding is validated by reactive site findings from Mulliken atomic charge distribution and molecule electrostatic potential surface studies. Information about distinct drug-receptor interactions obtained from molecular docking investigation offers the path of further study of molecular activity in various drug-receptor mechanism.

Comprehensive analysis of 2,5-dimethyl-1-(naphthalen-1-yl)-1H-pyrrole: X-ray crystal structure, spectral, computational, molecular properties, docking studies, molecular dynamics, and MMPBSA

This study examines the features of 2,5-dimethyl-1-(naphthalen-1-yl)-1H-pyrrole (DN1HP) in terms of its structure, vibrations, electronic transition properties, biological activity, and thermodynamic characteristics. X-ray single crystal structure solved and analysed. With the use of spectroscopic methods like FT-IR and UV–vis, the compound has been described. These experimental findings were contrasted with information derived from DFT (B3LYP) computations with the basis set 6–311++G(d,p). Vibrational allocations and Potential energy distribution(PED) were computed after optimizing the DN1PH compound's shape. The outcome of every experiment matched the values predicted by theory. To further investigate the reactivity, stability and biological activity of the titular molecule, calculations were made for the electrophilicity index (3.053), energy gap (3.789 eV), EH (−5.2962 eV), and EL (−1.5069 eV). To determine the compound's electrophilic and nucleophilic locations, a Molecular electrostatic potential (MEP) diagram was established. Molecular docking experiments have demonstrated the potential of the molecule in question as an anti-HIV medication. The binding energies of the drug to the proteins 3MLU, 3QEG, 5DHZ, and 3MLY are −5.86, −5.04, −5.01 and −4.97 kcal/mol, respectively. To further investigate the relationship and reliability of the protein (3MLU) with DN1HP, molecular dynamics (MD) simulators were utilized

Hydrogen bonding in 2,2,2-trifluoroethanol.

2,2,2-Trifluoroethanol (TFE) is known as a membrane mimetic solvent. The IR spectrum, 1H NMR spectrum, 13C NMR spin‒lattice relaxation times (T1), and nuclear Overhauser effect (NOE) data are consistent with extensive hydrogen bonding in TFE, but do not lead to structural features of the hydrogen bonding. Hence, DFT computations were carried out. The results predict the existence of a set of H-bonded dimers and trimers. The bond lengths and dihedral angles in these complexes are obtained, together with their dissociation energies. Computations were also performed for the geometry of the two conformers of the isolated monomer. The structure of one of the dimers consists of a 7-member cyclic fragment with a free CF3CH2 side chain. One set of the trimer structures involves the OH of a third monomer H-bonding to one of the F atoms in the CF3 group of the side chain of this dimer, thereby creating three trimer isomers. A fourth trimer cluster is formed from three monomers in which three OH∙∙∙O bonds create a cyclic fragment with three CF3CH2 side chains. The high dissociation energy (with respect to three monomers) indicates the high stability of the trimer complexes. The structural features of the trimer complexes resemble the structure of a conventional liquid crystal molecule and are postulated to resemble the latter in properties and function in solution, but at a much shorter timescale because of the noncovalent bonding. This hydrogen bonding phenomenon of TFE may be related to its function as a membrane memetic solvent. Initially, IR and NMR spectroscopic methods were used. Standard procedures were followed. For the computations, a hybrid DFT method with empirical dispersion, ωB97X-D, was used. The basis set, 6-311++G**, is of triple-ζ quality, in which polarization functions and diffuse functions were added for all atoms.