Vibrational Potential Energy Research Articles

Origin of the strong anharmonic-induced abnormal thermal conductivity in semiconductors

Abstract Semiconducting materials are the foundations of electronics and optoelectronics, and their heat management guides the design of highly efficient devices. For most semiconductors, the thermal conductivity of materials composed of light chemical species is higher than that of the iso-structured materials with heavy elements. For example, bulk Si shows a thermal conductivity higher than Ge. However, for many copper-based compounds, e.g. Cu halides, the thermal conductivity increases monotonously as the atomic number of halogens increases. On the other hand, for lead chalcogenides, the thermal conductivity of PbSe is lower than PbS and PbTe. In this work, we reveal that the combined effect of electronic states coupling and phonon collisions, giving rise to strong anharmonicity, is responsible for the abnormal trend of thermal conductivity of Cu halides and Pb chalcogenides. From CuCl to CuBr and CuI, the increasing thermal conductivity is due to the decreasing electronic coupling strength between Cu-occupied 3d and unoccupied 4s states when crystal symmetry is reduced, which leads to the increase of atomic vibrational potential energy and reduction of lattice anharmonicity. In Pb chalcogenides, the unusually lower thermal conductivity of PbSe than PbTe and PbS is mainly due to the intensive scattering between phonons caused by the localized transverse acoustic modes and soft optical modes, which outweigh the contribution of the crystal anharmonicity due to the anharmonic potential energy surface.

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

Investigating quantum coherence of N-methylpyrrole through vibrational spectroscopy and potential energy: A theoretical study

Quantum chemical calculations are utilized to analyze the potential causes of N-methylpyrrole oscillations, focusing on vibration spectra and potential energy curves. Optimization of the ground state, ionic state and 3s state structure reveal mostly sp2 hybridization. An analysis of the 3s state vibration spectrum and adiabatic binding energy indicate that changes in dihedral angles D2,3,4,1 and plane angle A3,2,1 are potential factors contributing to molecular oscillations. The role of vertical binding energy and adiabatic binding energy in the oscillation process are also discussed, shedding light on the possible dynamic processes of N-methylpyrrole.

Synthesis, characterization, and comprehensive computational analysis of aromatic hydrazone compounds: Unveiling quantum parameters, evaluating antioxidant activity, and investigating molecular docking interactions

This study presents a synergistic approach encompassing experimental synthesis, computational analysis, and antioxidant activity evaluation of two aromatic hydrazone compounds, namely 4-[(2E)-2-(2-nitrobenzylidene) hydrazinyl] benzoic acid (NBHZ) and 4-[(2E)-2-(2-hydroxybenzylidene) hydrazinyl] benzoic acid (HBHZ). Efficient synthesis yielded impressive quantities (70 % and 58 %, respectively), and structural characterization employed IR, UV–Vis, and NMR spectroscopy. Antioxidant potential was assessed using the DPPH free radical scavenging assay, revealing distinct capabilities of NBHZ and HBHZ, each featuring a nitro (NO2) and a hydroxy (OH) group, respectively, at the ortho position. HBHZ exhibited superior efficacy (IC50 = 1.15 μg/mL) compared to NBHZ (IC50 = 2.1 μg/mL) and the standard antioxidant BHT (IC50 = 1.83 μg/mL). Computational analyses using Gaussian 09 at the B3LYP/6–311 G(d,p) level elucidated electronic characteristics, molecular electrostatic potential (MEP), HOMO-LUMO energies, and global reactivity descriptors. VEDA 4 further investigated vibrational behavior and potential energy distribution (PED), topological analyses electron localization function (ELF), localized orbital locator (LOL), average localized ionization energy (ALIE), and reduced density gradient (RDG) were identified to evaluate their interactions. Thermochemical parameters explored antioxidant mechanisms (hydrogen atom transfer (HAT), single electron transfer–proton transfer (SET–PT), and sequential proton loss electron transfer (SPLET)). Molecular docking via iGEMDOCK revealed binding interactions with the target NADPH oxidase. These findings not only provide insights into the compounds' antioxidant potential but also underscore the impact of specific molecular features on their properties. This integrated approach contributes to advancing the understanding of hydrazone compounds, guiding the design of materials with tailored functionalities for applications in oxidative stress mitigation.

Quantum dynamics study of C—H stretching vibrational excitation in the F+CHD<sub>3</sub> → HF+CD<sub>3</sub> reaction

In recent decades, significant progress has been made in the precise theoretical investigation of gas-phase chemical reactions. Presently, a major challenge in the field of quantum dynamics is to develop the precise methodologies for studying chemical reactions involving more than four atoms. As a typical multi-atomic reaction system, the F+CH<sub>4</sub> reaction and its isotopic substitution reactions have attracted widespread attention from both experimental and theoretical perspectives in recent years. Experimental studies on the reaction of F+CHD<sub>3</sub> have revealed that the stretching vibration excitation of the C—H bond inhibits the bond dissociation, favoring the formation of DF+CHD<sub>2</sub> product channels. In this study, we use a seven-dimensional quantum time-dependent wave packet method to investigate the dynamics of the F+CHD<sub>3</sub> reaction in both the reactant vibrational ground state and the first stretching excited state of the C—H bond. In this work, the reaction probabilities under different vibrational conditions are analyzed, showing that when the collision energy is below 0.06 eV, the reaction probability curves exhibit numerous fast-oscillating peaks, supporting the experimentally suggested phenomena of dynamic resonance. In a collision energy range from 0.06 eV to 0.3 eV, the reaction probability for the HF product channel in the vibrational excited state is lower than that in the ground state, which is consistent with experimental observation. Through the analysis of the time-independent wave functions of product channels under low-energy collision conditions, it is found that for reactions involving vibrational ground states, the HF products in the product asymptotic region and the reaction transition state region are in the <i>v'</i> = 2 excited state and <i>v'</i> = 3 excited state of stretching vibration, respectively, which are consistent with previous experimental observations and six-dimensional quantum wave packet simulations. For reactions involving the first excited state of C—H stretching vibration, the HF products in the product asymptotic region and the reaction transition state region are both in the <i>v'</i> = 3 excited state of stretching vibration, which are consistent with the results obtained based on energy analysis. Simulation results indicate that in the case of low-energy collisions, the time-independent wave function for the C—H stretching vibrational excited state tends to be closer to the D atom side in the transition state region. This phenomenon is attributed to the more significant energy advantage of the vibrational excited state potential energy surface in the large collision angle region, explaining the inhibitory effect of stretching vibration excitation on the HF product channel. This study offers important theoretical support for explaining experimental results and contributes to a more in-depth understanding of the influence of vibrational mode excitations on the dynamical processes in poly-atomic reactions.

Synchrotron-based UV resonance Raman spectroscopy probes size confinement, termination effects, and anharmonicity of carbon atomic wires

Vibrational and electronic properties and anharmonicity of sp-carbon atomic wires (i.e., polyynes) have been studied using resonance Raman spectroscopy, focusing on the confinement effects connected to their structure (length and termination). We exploited the fine tunability of the synchrotron radiation to resonantly excite short H-, CH3-, and CN-capped carbon atomic wires at their vibronic transitions in the deep UV. We report for the first time the resonance Raman spectra of size-selected CH3-capped polyynic wires (HCnCH3, n = 8–12) and CN-capped wires (HC6CN and HC12CN). We observed that the degree of π-electron conjugation increases with the wire length and is related to the specific termination. The analysis of multiple quanta Raman overtone bands shows that the anharmonic correction of the vibrational potential energy becomes increasingly relevant as the wire length increases. Finally, studying the vibronic lines of the UV absorption spectra allows the determination of an effective displacement parameter between the minima of the ground and the low-lying excited state, proving that the strong electron-phonon coupling of these systems is sensitive to chain length and termination.

The importance of electron correlations on vibrational anharmonicities and potential energy surfaces

An assessment and importance of different‐order of electron correlation effects on anharmonic vibrational potential energy surfaces (PESs) is reported. Systematic construction of quadratic, cubic and quartic force-fields using CCSD(T), MP2 and HF methods are performed for anharmonic vibrational spectroscopic calculations. The accuracies and convergences are assessed for VPT2 and VCI methods. The level of electron correlation is found important for the accuracies of harmonic force-constants while its effects on anharmonicities are less significant. Following this, suitable hybrid PESs are suggested for better accuracy/cost ratio. For the hybrid PESs, a more accurate high-level and less accurate low-level electron- correlation methods are employed to compute the harmonic and anharmonic part of the potential, respectively. The estimated deviations for hybrid PESs are found a few wavenumbers with the highly correlated methods as well as experiment. That in turn shows the validity and applicability of such hybrid PESs for large molecular systems.

Theoretical study on the vibrational spectra and potential energy curves for SiC ([formula omitted]) and SiS ([formula omitted]) molecules

In this work, the vibrational constants (ωe,ωexe) calculated by the variational algebraic method (VAM) and some other molecular constants (De,re,Be,αe) were used to construct the improved Hulburt–Hirschfelder (IHH) analytical potential energy function (APEF). Not only that, but the calculated VAM potential points are used as the ’true’ energies to determine the value of the variational parameter λ which is the pivotal fitting parameter in the IHH potential. With limited experimental data, high-precision IHH potential can be achieved by combining the VAM and the IHH APEF. This combination of the VAM and the IHH APEF is referred to be VAIHH APEF, which is employed to study the vibrational energies and potential energy curves (PECs) of SiC (X3Π) and SiS (X1Σ+) molecules, yielding full vibrational spectra and spectroscopic constants. The calculational results indicate that the VAIHH APEFs of SiC (X3Π) and SiS (X1Σ+) molecules are in good agreement with the experimental RKR potential points. Accurate PECs of SiC (X3Π) and SiS (X1Σ+) molecules imply that the VAIHH APEF is of high quality.

Structural and spectroscopic analysis of L‐Proline monomer and dimer by DFT approach

AbstractIn this work we have analyzed the Fourier Transform Infrared (FTIR), Raman and Surface Enhanced Raman Spectra (SERS) of L‐Proline. The molecule under consideration L‐Proline in monomer and dimer states were optimized using DFT/B3LYP and DFT/M06‐2X methods with 6‐31G (d,p) basis set. In order to correlate the experimental SERS spectra we have calculated the Raman spectra of L‐Proline monomer and dimer with silver (Ag) clusters using Density Functional Theory (DFT) with B3LYP functional and LANL2DZ basis set. The vibrational spectra were interpreted by using vibrational energy distribution analysis (VEDA) program and potential Energy Distribution (PED) analysis of the vibrational modes have been performed to have a clear picture of the fragments of different states of the molecule. The equilibrium molecular geometry, harmonic vibrational wavenumbers, Frontier molecular orbitals, Mulliken charges, energy parameters and various bonding features have also been computed.

The Importance of Electron Correlations on Vibrational Anharmonicities and Potential Energy Surfaces

The Importance of Electron Correlations on Vibrational Anharmonicities and Potential Energy Surfaces

Energy conversion during electrically actuated jumping of droplets

Many industrial technologies, such as condensation cooling and fuel cells, require solid-liquid separation. Electrowetting is a very effective method of inducing droplets to detach from hydrophobic surfaces, and it is very convenient to control. The jumping of droplets excited by an electric field depends on the conversion of surface energy into kinetic energy and other forms of energy. At present, there is still a lack of in-depth research on this process. In this study, a high-speed camera is used to capture the jumping motion of a droplet on a hydrophobic surface under the actuation of electrowetting, and the threshold voltage that causes the droplet to detach is estimated based on the changes in contact angle and droplet shape. A self-written Matlab program is used to analyze and calculate the various forms of energy in the process of droplets detaching and subsequent bouncing. The results show that there is an obvious coupling relationship between the kinetic energy and potential energy of the droplet’s center of mass during the flight of the droplet from the surface. The vibrational kinetic energy and surface potential energy also show a certain coupling relationship during the flight phase. The internal dissipation caused by the viscosity of the droplet increases with the droplet oscillation amplitude increasing, and decays with time. Because it can cause the droplet to oscillate and deform and create more surface energy, AC pulses are more efficient than direct current in the droplet bounce. By revealing the energy conversion and dissipation mechanism in the process of droplet jumping driven by electrowetting, a theoretical reference is provided for the application of this technology in solid-liquid separation and three-dimensional digital microfluidics.

Synthesis of Schiff base (E)-4-((2-hydroxy-3,5-diiodobenzylidene)amino)-N-thiazole-2-yl)benzenesulfonamide with antimicrobial potential, structural features, experimental biological screening and quantum mechanical studies

We report the synthesis and characterisation of the Schiff base (E)-4-((2-hydroxy-3,5-diiodobenzylidene)amino)-N-thiazole-2-yl) benzene sulfonamide (DITH) prepared the by condensation of 3,5-diiodosalicylaldehyde and sulfathiazole. The synthesised compound was characterised with spectral techniques like FTIR, 1HNMR and UV-Visible spectroscopy. The molecule was optimised using computational methods employing DFT/B3LYP/cc-pVDZ/Lanldz(I) basis sets followed by the simulation of the vibrational spectra, scaled and compared with experimental spectra for vibrational assignment and potential energy distribution. The 1HNMR calculated from the standard GIAO method with DMSO as a solvent was also compared with experimental spectra. The UV-Vis spectrum calculated using TD-DFT/CAM-B3LYP/cc-pVDZ/Lanl2dz(I). Wave function based properties like localised orbital locator, electron localisation function and non-covalent interactions has been studied extensively. The compound DITH's pharmacodynamic indicated that the compound has excellent drug-likeness properties. Prediction of the activity and structure spectra (PASS) studies predicted that it has anti-infective properties, confirmed by a docking score of -7.1 and -7.2 kcal/mol for antibacterial and antifungal properties. Experimental studies show that the newly synthesised Schiff base shows significant inhibition of bacteria and fungi growth compared to standard drugs.

The Gibbs Energy–Potential Energy Conundrum and Chemical Reactivity: Implications for Catalysis and Enzyme Action

The interpretation of transition state theory via reaction energy profiles is problematical, as it remains unclear whether the energy being represented is the Gibbs energy or the potential energy. Although transition state theory is formally an extension of classical equilibrium theory, employing the Gibbs energy can lead to ambiguities in explaining reactivity trends and differences. Thus, the differential reactivity of the carbonyl group in carboxylic esters and carboxylic acid chlorides, when present in the same molecule, can only be explained by invoking transition state effects because of the common ground state. The said transition state effects, however, apparently need implausible assumptions.
 It is argued herein that these ambiguities can be avoided by employing potential energy. In particular, by invoking the “localized” potential energy at a reactive center, ground state effects can be brought into play. This is likely to be largely vibrational potential energy, as this is closely involved in bond breaking and making. It appears, therefore, that transition state theory is best viewed in a qualitative sense for it to be practically meaningful.
 These arguments, in fact, have intriguing implications for catalysis, particularly the theory of enzyme catalysis. Thus, enzymes apparently possess large negative Gibbs energies of formation, hence their reactivity cannot be explained by ground state effects. However, if the “localized” potential energy of the reactive groups in the active site is considered, the phenomenal reactivity of enzymes becomes comprehensible, in an alternative to the Pauling hypothesis of transition state stabilization. This generally implies that the action of catalysts needs to take into account the ground state potential energy of the catalyst, which is almost always ignored in current theoretical treatments.

Elaborated molecular structure, molecular docking and vibrational spectroscopic investigation of N-((4-aminophenyl)sulfonyl)benzamide with Density functional theory

Abstract The molecule N-((4-aminophenyl)sulfonyl)benzamide was optimized by making use of density functional theory (DFT) with 6-311++G(d,p) basis set. The vibrational frequency and potential energy distribution (PED) of the title compound were calculated and compared with experimental calculations. By using DFT method, the reactivity nature of the molecule was characterized, like as Local reactivity descriptor, Natural bond orbital with a basis set of 6-311++G(d,p), Frontier molecular orbital (FMOs), etc. The electronic properties for HOMO-LUMO, UV-Vis and MEP maps were contemplated by IEFPCM model with various solvation impacts which depends on TD-DFT ((B3LYP for HOMO-LUMO, MEP and M062X for UV)/6-311++G(d,p)) strategies. The Molecular docking analysis reveals the inhibitory nature of title molecule with Aspergillus Niger a fungal protein, SARS CoV-1 and SARS CoV-2 viral proteins. Hence, the present study reveals that the title compound has structural behavior and bioactive (antifungal and antiviral) nature.

Spectroscopic, quantum chemical, hydrogen bonding, reduced density gradient analysis and anti-inflammatory activity study on piper amide alkaloid piperine and wisanine

A combined experimental and theoretical quantum chemical calculations have been carried out to study the geometry, vibrational wavenumbers, electronic transition and anti-inflammatory activity of piper amide alkaloid compound piperine (PP). Computational study is done on other piper amide alkaloid wisanine (WS) using B3LYP/6–311G(d,p) basis set. The conformational analysis is carried out to find the most stable geometry of PP and WS. Normal coordinate analysis (NCA) is performed to analyse the vibrational wavenumber and potential energy distribution (PED) assignments. The interaction of PP and WS with water molecule is also performed to know the effect of hydrogen bond on its geometry and vibrational spectra. Natural bond orbital (NBO) analysis was performed to study the charge delocalization, hyperconjugative interaction, inter and intramolecular hydrogen bonding interaction in the molecule to know about anti-inflammatory active site. Non-covalent interactions are analyzed using reduced density gradient (RDG) analysis. The UV–visible spectrum of PP in ethanol and water solvent is recorded and compared with calculated data. The 1H and 13C NMR spectra of PP are recorded and analyzed. The chemical stability and anti-inflammatory activity of title compound are evaluated by HOMO-LUMO analysis. The chemical reactivity descriptors are calculated to predict the reactivity and stability of the molecule. The intermolecular interactions and crystal packing of title compound are studied by Hirshfeld surface analysis techniques. PP is screened for its anti-inflammatory activity. Molecular docking study predicts the binding site of PP and WS into its target protein.

Quantum computational, spectroscopic and molecular docking studies of 5,5-dimethylhydantoin and its bromine and chlorine derivatives

Abstract Quantum computational and spectroscopic studies are very much essential to study the molecular structure, functional group present, quantum level properties, and applications of organic compounds. In this research experimental spectroscopic studies like FT-Raman, FT-IR, UV–Visible, and density functional theory (DFT) approach are followed on the bromine and chlorine derivatives of 5,5-dimethylhydantoin. The experimental results of FT-IR, FT-Raman, and UV–Vis are compared with the theoretical calculations like density functional theory with the B3LYP method and 6–311++G(d,p) basis set. The optimized molecular geometry of the two derivatives is carried out compared with the experimental studies. The vibrational assignments and potential energy distribution were reported. This work also provides the non-linear optical properties. The stability and reactive nature of the compounds were calculated by natural bond orbital analysis. The bonding nature and bond energies are computed by atoms in a molecule theory. The electronic properties like HOMO- LUMO and various other chemical properties are obtained using B3LYP and also CAM-B3LYP methods with 6–311++G(d,p) basis set. By using the UV–Vis experimental studies and time-dependent theoretical studies the maximum absorption wavelength, bandgap, and transition assignments were carried out with different solvents. The reactive areas of the bromine and chlorine derivatives were obtained using molecular electrostatic potential and Fukui function studies. The ligand and protein interactions are computed by molecular docking to identify the drug activities.

Experimental and Theoretical Vibrational Spectroscopic Analysis of Etoricoxib

Abstract Etoricoxib is one of the non-steroidal anti-inflammatory drug used primarily in the treatment of various types of arthritis. In this work, the vibrational analysis of etoricoxib molecule has been presented using density functional theory calculations. Fourier transform Infra-red and Raman spectra of the inspected molecule have been reported in the regions 4000-400 cm-1 and 1800-100 cm-1, respectively. The observed bands have been compared with the calculated wavenumbers, yielding good agreement. To have a better understanding of the vibrational spectra of etoricoxib and to identify the key vibrational bands, the complete assignments of fundamental vibrations have also been performed on the basis of calculated vibrational wavenumbers and potential energy distribution analysis of the vibrational modes.

Invivo, molecular docking, spectroscopy studies of (S)-2,3-Dihydro-5,7-dihydroxy-2(3-hydroxy-4-methoxyphenyl)-4H-1-benzopyran-4-one: A potential uptake PI3/AKT inhibitor

Abstract The molecule (S)-2,3-Dihydro-5,7-dihydroxy-2(3-hydroxy-4-methoxyphenyl)-4H-1-benzopyran-4-one (Hesperetin) was optimized utilizing density functional theory (DFT) with B3LYP/6-311G(d,p) basis set. The vibrational frequencies and potential energy distribution (PED)% of Hesperetin molecule was computed and it shows good agreement with the experimental values. The reactivity nature of the molecule was analysed with various DFT methods such as local reactivity descriptors, Molecular Electrostatic Potential (MEP) and Frontier Molecular orbitals (FMOs). Drug likeness and ADMET properties were analysed for the prediction of pharmacokinetic properties like Absorption, Distribution, Metabolism, Excretion and Toxicity. The molecular docking analysis reveals that inhibitory nature of the Hesperetin molecule. Various signalling pathways are regulating the lung cancer progression including PI3K/AKT. Interrupting this signalling pathway could help us discover the new drug derivatives. Hence, the present study reports the structural details, intermolecular interactions of PI3K and Hesperetin and the toxicity study (in vivo) was also analysed by inhibition of human lung cancer cells (A549) proliferation.

Strong-field Fourier transform vibrational spectroscopy of methanol cation and its isotopologues using few-cycle near-infrared laser pulses

ABSTRACTPump-probe measurements of methanol and its isotopologues (CH3OH, CH3OD and CD3OH) were performed using near-infrared few-cycle intense laser pulses. The yields of the parent ion and the fragment ions oscillate as a function of the pump-probe time delay, reflecting the time evolution of the vibrational wave packet created in methanol and methanol cation by the pump pulse. By the Fourier transform (FT) of the time-domain data, the vibrational mode frequencies of methanol and methanol cations were determined on the basis of the assignment of the peak profiles in the FT spectra made using their relative phases and the theoretical vibrational frequencies and potential energy distributions.

A computational and spectroscopic interpretation (FT-IR, FT-Raman, UV–vis and NMR) with molecular docking studies on 3-carboxy-2-hydroxy-N, N, N-trimethyl-1-propanaminium hydroxide: A pharmaceutical drug

Abstract An Antidote drug 3-carboxy-2-hydroxy-N,N,N-trimethyl-1-propanaminium hydroxide (C7H16NO3) has been used in this work to investigate the vibrational frequencies using FT-IR, FT-Raman UV–vis and NMR spectra experimentally and quantum chemical calculations of the scaled frequencies using DFT B3LYP/6-311++G(d,p)basis set compared theoretically. In order to assign vibrational wavenumbers Potential Energy Distribution (PED) has been carried out. The Natural bond orbital (NBO) analysis of this molecule has been carried out to describe the various intra molecular interactions responsible for the stabilization of the molecule. Local reactivity properties of the title molecule have been executed through molecular electrostatic potential (MEP).The HOMO and LUMO energy gap were performed using TD-DFT theory and the differences are compared with UV-absorption spectra. The statistical thermodynamical functions (Entropy, Enthalpy and Heat capacity) have been calculated for the range of 100–1000 K. The Fukui functions are evaluated to describe the activity of the sites and Molecular docking study has been executed to investigate the potential of the title molecule to bind with 1S5O receptor, an antidote protein.