Article
Chemistry, Physical
Jessica Bowles, Sascha Jahnigen, Rodolphe Vuilleumier, Florent Calvo, Carine Clavaguera, Federica Agostini
Summary: The vibrational spectrum of alanine amino acid was computationally determined in different environments and phases using molecular dynamics trajectories and an optimized polarizable force field. The analysis revealed significant differences between the spectra of neutral and zwitterionic forms of alanine in the gas phase, and provided insights into the molecular origins of vibrational bands in condensed phases.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Tao E. Li, Abraham Nitzan, Joseph E. Subotnik
Summary: Recent experiments have shown that the properties of molecules can be altered inside an optical Fabry-Perot microcavity under collective vibrational strong coupling conditions, but this phenomenon is not yet well understood theoretically. By studying the effect of the cavity environment on the nonlinear optical response of the molecular subsystem, researchers have found that a strong excitation pulse to the lower hybrid light-matter state leads to significantly enhanced molecular nonlinear absorption within the cavity. This polariton-enhanced multiphoton absorption also results in an ultrashort polariton lifetime under strong illumination. The mechanism by which energy is transferred to higher vibrationally excited dark states is expected to be observed experimentally in different molecular systems and cavities.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
G. Venkatesh, Yudibeth Sixto-Lopez, P. Vennila, Y. Sheena Mary, Jose Correa-Basurto, Y. Shyma Mary, A. Manikandan
Summary: This study investigates the properties of 2-deoxy-D-glucose and its interactions with metal clusters using the DFT method. It is found that stable clusters can form between 2-deoxy-D-glucose and transition metal clusters of copper, silver, and gold. The stability and chemical properties of 2-deoxy-D-glucose are strongly influenced by the size of the clusters. Molecular electrostatic potential maps provide insight into the chemical reactivity and intermolecular interactions. Molecular docking and molecular dynamic simulation analyses suggest that the compound has potential activity against cancer, SARS-CoV-2, and SARS-CoV.
JOURNAL OF MOLECULAR STRUCTURE
(2022)
Article
Nuclear Science & Technology
S. Giusepponi, F. Buonocore, M. Celino, M. Lupo Pasini, A. Frattolillo, S. Migliori
Summary: Research on the injection of high-speed cryogenic pellets made of frozen hydrogen-isotopes and very large pellets composed of cryogenic solid with suitable impurities has shown effectiveness in fueling magnetically confined thermonuclear fusion plasmas and reducing damage risks. Pipe gun injectors are reliable and commonly used devices for this purpose.
FUSION ENGINEERING AND DESIGN
(2022)
Article
Polymer Science
Carlo Andrea Massa, Francesco Puosi, Antonio Tripodo, Dino Leporini
Summary: The vibrational dynamics of a model polymer glass is studied using Molecular Dynamics simulations, focusing on the soft monomers and their tendency to form quasi-local clusters with strong anisotropy in shape. Limited size systems were used to better understand the role of these soft monomers.
Article
Biochemistry & Molecular Biology
A. Saral, P. Sudha, S. Muthu, Ahmad Irfan
Summary: The title compound 5-isoquinolinesulfonic acid (5IQSA) is characterized using various spectroscopic techniques, and important parameters such as molecular geometry, vibrational frequencies, and infrared intensities are calculated using Density Functional Theory. The study also investigates the UV-Vis spectra, molecular dynamics, NLO behavior, and topological properties of the compound.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Analytical
Tatiana Zolotoukhina, Momoko Yamada, Shingo Iwakura
Summary: Surface-enhanced Raman scattering (SERS) nanoprobes have great potential in in vivo imaging and can be used as nanobiosensors for DNA and protein identification experiments. Faster imaging in real-time is required due to the multiple spectrum acquisition of Raman scanners, while the weak signal of SERS necessitates averaging of acquired spectra. Establishing spectral libraries through simulating measurement conditions relative to enhancer nanostructures is crucial for research.
Article
Chemistry, Physical
J. R. C. Santos, P. E. Abreu, J. M. C. Marques
Summary: This study employed molecular dynamics simulations to calculate diffusion coefficients of various pesticides, with comparisons to experimental data revealing some errors, which were rationalized in terms of solute-solvent interactions.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Astronomy & Astrophysics
Bilel Mehnen, Ignacio Suarez Martin, Evelyne Roueff, Majdi Hochlaf, Gunnar Nyman
Summary: Based on ab initio electronic structure data, parametrized analytic potential energy surfaces for HCN and HNC isomers are developed by variationally calculating rovibrational energy levels and adjusting potential parameters. An analytic expression is determined to effortlessly calculate the rovibrational energy levels. The obtained empirical potentials are used to calculate rovibrational levels for multiple isotopologues, and the accuracy is estimated based on comparison with experimental results. Molecular parameters and endo- and exoergicities for isotopic exchange reactions are also given.
MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY
(2022)
Article
Chemistry, Physical
Johan Aqvist, Florian van der Ent
Summary: This study investigates the impact of heat capacity changes on temperature optima in enzyme catalysis, proposing methods to calculate the activation free energy's temperature dependence and absolute heat capacities of reactants and transition states through molecular dynamics simulations. It also provides a new scheme for calculating absolute heat capacity changes.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Julien Deveimy, Alain Dequidt, Patrice Malfreyt
Summary: In this study, we utilize different methodologies including thermodynamic integration (TI), free energy perturbation (FEP), and potential of mean force (PMF) to calculate the free energy of adsorption. A model system is designed to reduce the dependence on phase space sampling and pathway choice. The reliability and efficiency of these simulations are confirmed through a thermodynamic cycle, and free energy contributions related to desorption and solvent desolvation are calculated. The agreement between different calculations of adsorption free energy provides quantitative data for understanding the energy contributions in adsorption processes.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Applied
Mark A. Burton, Brad A. Steele, Jonathan C. Crowhurst, Ana Racoveanu, I-Feng W. Kuo, William L. Shaw, Richard H. Gee
Summary: Incorporating isotopically labelled materials in degradation experiments can help understand the mechanism of decomposition. Characterizing synthesized isotopologues requires understanding the observable signals affected by isotopic substitution. Vibrational spectroscopy is an ideal technique to evaluate isotopic variants as it can distinguish between them.
PROPELLANTS EXPLOSIVES PYROTECHNICS
(2023)
Article
Multidisciplinary Sciences
Shima Taherivardanjani, Roman Elfgen, Werner Reckien, Estela Suarez, Eva Perlt, Barbara Kirchner
Summary: The study presents the scaling behavior of ab initio molecular dynamics simulations for different sized bulk systems of liquid methanol and analyzes the performance characteristics on either a local compute cluster or a supercomputer. Additionally, the influence of different parameters on the quality of infrared and Raman spectra is investigated using various simulation frameworks. The results guide future experimental and theoretical researchers to gain a profound understanding of vibrational spectra, which enhances the elucidation of molecular structure.
ADVANCED THEORY AND SIMULATIONS
(2022)
Article
Multidisciplinary Sciences
N. Gao, Z. W. Yao, G. H. Lu, H. Q. Deng, F. Gao
Summary: The study found a new diffusion mechanism for <100> interstitial dislocation loops in BCC iron using self-adaptive accelerated molecular dynamics, which represents a significant step towards understanding the mechanical behavior and microstructure evolution of the material.
NATURE COMMUNICATIONS
(2021)
Article
Spectroscopy
Pengxu Ran, Genggeng Li, Huaming Hou
Summary: Laser ablation molecular isotopic spectrometry (LAMIS) was utilized to quantitatively analyze the isotopic ratio OD/OH in laser induced plasma from water samples, demonstrating high efficiency and accuracy. A theoretical spectral fitting model was developed for OD and OH molecules, enabling precise extraction of isotopic ratios and showing a linear relationship between D concentration and D2O concentration. These findings highlight the advantages of LAMIS in isotopic quantitative analysis under ambient conditions.
SPECTROCHIMICA ACTA PART B-ATOMIC SPECTROSCOPY
(2021)
Article
Chemistry, Physical
Martina Kaledin, John M. Moffitt, Craig R. Clark, Fareeha Rizvi
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2009)
Article
Chemistry, Physical
Martina Kaledin, Christopher A. Wood
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2010)
Article
Chemistry, Physical
Reagan Hooper, Dalton Boutwell, Martina Kaledin
JOURNAL OF PHYSICAL CHEMISTRY A
(2019)
Article
Chemistry, Physical
Dalton Boutwell, Onyinye Okere, Oluwaseun Omodemi, Alexander Toledo, Antonio Barrios, Monique Olocha, Martina Kaledin
JOURNAL OF PHYSICAL CHEMISTRY A
(2020)
Article
Chemistry, Physical
Dominick Pierre-Jacques, Ciara Tyler, Jason Dyke, Alexey L. Kaledin, Martina Kaledin
Summary: A novel variant of the driven molecular dynamics (DMD) method has been developed for probing Raman active vibrations, with numerical results using first-principles calculations for vibrational fundamentals presented and discussed. This method allows identification and assignment of all Raman active vibrational modes, including anharmonic corrections, by means of trajectory analysis. It is well suited for ab initio dynamics implementation, requiring only one element of the full polarizability tensor and its nuclear derivative for an alpha-DMD trajectory.
Article
Chemistry, Physical
Oluwaseun Omodemi, Sarah Sprouse, Destyni Herbert, Martina Kaledin, Alexey L. Kaledin
Summary: An analytic Cartesian representation of the molecular dipole polarizability tensor surface is constructed using polynomials in interatomic distances, based on ab initio data points obtained from a molecular dynamics simulation. The formulation is shown to be free of singularities, symmetric, translationally invariant, and nonreliant on a body-fixed coordinate system. Permutational invariance of like nuclei is demonstrated, making the approach useful for highly fluxional and reactive systems.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Dalton Boutwell, Dominick Pierre-Jacques, Olivia Cochran, Jason Dyke, Dayana Salazar, Ciara Tyler, Martina Kaledin
Summary: This study investigates the vibrational coupling and proton-transfer motion of the hydrogen oxalate anion using first-principles molecular dynamics (MD) and dipole-driven molecular dynamics (mu-DMD) simulations. The results show that low-frequency bending and stretching vibrations of CO2 and CCO play a crucial role in shortening the OmiddotmiddotmiddotO distance and promoting proton transfer. Resonant mu-DMD trajectories reveal a complex spectral feature involving the combination of various modes and their overtones.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Article
Chemistry, Multidisciplinary
Oluwaseun Omodemi, Martina Kaledin, Alexey L. Kaledin
Summary: This article describes a linear parameterization method for the Cartesian representation of molecular dipole polarizability tensor surfaces. The method has competitive levels of computational complexity, accuracy, and uniqueness in solving the problem.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2022)
Article
Chemistry, Physical
Oluwaseun Omodemi, Ramsay Revennaugh, Janiyah Riley, Alexey L. Kaledin, Martina Kaledin
Summary: This research presents molecular dynamics simulations, polarizability driven MD simulations, and pump-probe simulations of Raman spectra for N4H+ and its isotopologues. By utilizing Permutationally Invariant Polynomials (PIPs), a CCSD(T)/aug-cc-pVTZ-tr(N:spd, H:sp) polarizability tensor surface (PTS) was derived for the first time. The results reveal the potential applications of this method in studying the unique properties of nitrogen-hydrogen bonds.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
M Kaledin, AL Kaledin, JM Bowman
JOURNAL OF PHYSICAL CHEMISTRY A
(2006)
Article
Chemistry, Physical
M Kaledin, A Brown, AL Kaledin, JM Bowman
JOURNAL OF CHEMICAL PHYSICS
(2004)
