Search results for "Computational Chemistry"
showing 9 items of 1209 documents
On the biradicaloid nature of long quinoidal oligothiophenes: experimental evidence guided by theoretical studies.
2007
ChemInform Abstract: Assignment of the Absolute Configuration and Total Synthesis of (+)-Caripyrin.
2015
The antifungal secondary metabolite (+)-caripyrin was studied by vibrational circular dichroism spectroscopy. Analysis of the recorded data, with the Boltzmann weighted-average of the spectra calculated at the B3LYP/6-311G(d,p) level of theory for all relevant conformers, unequivocally proved the (R,R)-configuration for the dextrorotatory natural product. Based on this finding, a short enantioselective synthesis of (+)-caripyrin was developed.
Role of Vibrational Dynamics in Electronic Relaxation of Cr(acac)3
2015
Ultrafast energy relaxation of Cr(acac)3 dissolved in tetrachloroethylene (TCE) is studied by time-resolved infrared (TRIR) spectroscopy by using electronic and vibrational excitation. After electronic excitation at 400 or 345 nm, the ground state recovers in two time scales: 15 ps (major pathway) and 800 ps (minor pathway), corresponding to fast electronic transition to the ground state and intermediate trapping on the long-lived (2)E state followed by intersystem crossing (ISC) to the ground state. The quantum yield for the fast recovery of the ground state depends on the excitation wavelength, being higher for 345 nm. Vibrational cooling (VC) occurs on the electronic excited states with …
A Unified AMBER-Compatible Molecular Mechanics Force Field for Thiolate-Protected Gold Nanoclusters.
2016
We present transferable AMBER-compatible force field parameters for thiolate-protected gold nanoclusters. Five different sized clusters containing both organo-soluble and water-soluble thiolate ligands served as test systems in MD simulations, and parameters were validated against DFT and experimental results. The cluster geometries remain intact during the MD simulations in various solvents, and structural fluctuations and energetics showed agreement with DFT calculations. Experimental diffusion coefficients and crystal structures were also reproduced with sufficient accuracy. The presented parameter set contains the minimum number of cluster-specific parameters enabling the use of these p…
Force Distribution Analysis of Mechanochemically Reactive Dimethylcyclobutene
2013
Internal molecular forces can guide chemical reactions, yet are not straightforwardly accessible within a quantum mechanical description of the reacting molecules. Here, we present a force-matching force distribution analysis (FM-FDA) to analyze internal forces in molecules. We simulated the ring opening of trans-3,4-dimethylcyclobutene (tDCB) with on-the-fly semiempirical molecular dynamics. The self-consistent density functional tight binding (SCC-DFTB) method accurately described the force-dependent ring-opening kinetics of tDCB, showing quantitative agreement with both experimental and computational data at higher levels. Mechanical force was applied in two different ways, namely, exter…
The Role of the Anchor Atom in the Ligand of the Monolayer-Protected Au25(XR)18– Nanocluster
2015
We present a density functional theory (DFT) investigation on the role of the anchor atom and ligand on the structural, electronic, and optical properties of the anionic Au25(XR)18– nanocluster (X = S, Se, Te; R = H, CH3, and (CH2)2Ph). Substituting the anchor atom with other group 16 elements induces subtle changes in the Au–Au and Au–X bond lengths and polarization of the covalent bond. The changes in the electronic structure based on substituting both the anchor and R groups are presented through careful analysis of the density of states and theoretical determined optical spectra. We give a detailed side-by-side comparison into the structural, electronic, and optical properties of Au25(X…
Crystal Structures and Density Functional Theory Calculations of o-and p-Nitroaniline Derivatives: Combined Effect of Hydrogen Bonding and aromatic i…
2013
The interplay of strong and weak hydrogen bonds, dipole–dipole interactions, and aromatic interactions of o- and p-nitroaniline derivatives was studied by combining crystal structure analysis and density functional theory (DFT) calculations. Crystal structures of four 2-nitroaniline derivatives, 2-((2-nitrophenyl)amino)ethyl methanesulfonate (1A), 2-((2-nitrophenyl)amino)ethyl 4-methylbenzenesulfonate (2A), N,N′-((1,3-phenylenebis(oxy))bis(ethane-2,1-diyl))bis(2-nitroaniline) (3A), and N-(2-chloroethyl)-2-nitroaniline (4A), and crystal structures of three 4-nitroaniline derivatives, 2-((4-nitrophenyl)amino)ethyl methanesulfonate (1B), 2-((4-nitrophenyl)amino)ethyl 4-methylbenzenesulfonate (…
Mechanisms of irreversible aquaporin-10 inhibition by organogold compounds studied by combined biophysical methods and atomistic simulations
2021
Abstract The inhibition of glycerol permeation via human aquaporin-10 (hAQP10) by organometallic gold complexes has been studied by stopped-flow fluorescence spectroscopy, and its mechanism has been described using molecular modelling and atomistic simulations. The most effective hAQP10 inhibitors are cyclometalated Au(III) C^N compounds known to efficiently react with cysteine residues leading to the formation of irreversible C–S bonds. Functional assays also demonstrate the irreversibility of the binding to hAQP10 by the organometallic complexes. The obtained computational results by metadynamics show that the local arylation of Cys209 in hAQP10 by one of the gold inhibitors is mapped int…
On the ‘expanded local mode’ approach applied to the methane molecule: isotopic substitutions CH3D ←CH4 and CHD3 ←CH4
2014
Operator perturbation theory and the symmetry properties of the axially symmetric XYZ3 (C3v) type molecules are used for the determination of the spectroscopic parameters in the form of functions of structural parameters and parameters of the intramolecular potential function. Several relations between sets of spectroscopic parameters of these molecules are obtained. The ‘expanded local mode’ model and the general isotopic substitution theory are used to estimate the relations between spectroscopic parameters of CH3D and CHD3, on one hand, and with the Td symmetric isotopic species, CH4, on the other hand. Test calculations with the isotopic relations show that even without including prior …