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Register a new userElectrostatic Potential as a Descriptor of Anti-Bacterial Activities of Some Anacardic Acid Derivatives: A Study Using Density Functional Theory
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Structures and minimum molecular electrostatic potential (MEP) distributions in anacardic acid and some of its derivatives have been studied by full geometry optimization at the M06-2X/6-31G(d,p), WB97XD/6-31G(d,p) and B3LYP/6-31G(d,p) levels of density functional theory (DFT) in gas phase as well as in DMSO and aqueous solutions. Solvent effect was treated employing the integral equation formalism of the polarizable continuum model. Effects of modifications of the C1-side chain on the minimum MEP values in various regions were studied. Minimum MEP values near the oxygen atoms of the C2-OH group, oxygen or sulfur atoms of the C1-attached urea or thiourea groups and above or below the ring plane considered to be involved in interaction with the receptor were used to perform multiple linear regression. Experimentally observed anti-bacterial activities of these molecules against S. aureus are thus shown to be related to minimum MEP values in the above mentioned regions. Among the three DFT functionals used in the study, the M06-2X functional is found to yield most reliable results. Anti-bacterial activities have been predicted for certain molecules of the class which need to be verified experimentally.
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Hydrogen bonds (HBs) play a crucial role in the physicochemical properties of ionic liquids (ILs). At present, HBs between cations and anions (Ca-An) or between cations (Ca-Ca) in ILs have been reported extensively. Here, we provided DFT evidences for the exists of HBs between anions (An-An) in the IL 1-(2-hydroxyethyl)-3-methylimidazolium 4-(2-hydroxyethyl)imidazolide [HEMIm][HEIm]. The thermodynamics stabilities of anionic, cationic, and H2O dimers together with ionic pairs were studied by potential energy scans. The results show that the cation-anion pair is the most stable one, while the HB in anionic dimer possesses similar thermodynamics stability to the water dimer. The further geometric, spectral and electronic structure analyses demonstrate that the inter-anionic HB meets the general theoretical criteria of traditional HBs. The strength order of four HBs in complexes is cation-anion pair > H2O dimer = cationic dimer > anionic dimer. The energy decomposition analysis indicates that induction and dispersion interactions are the crucial factors to overcome strong Coulomb repulsions, forming inter-anionic HBs. Lastly, the presence of inter-anionic HBs in ionic cluster has been confirmed by a global minimum search for a system containing two ionic pairs. Even though hydroxyl-functionalized cations are more likely to form HBs with anions, there still have inter-anionic HBs between hydroxyl groups in the low-lying structures. Our studies broaden the understanding of HBs in ionic liquids and support the recently proposed concept of anti-electrostatic HBs.
The present work proposes to use density-functional theory (DFT) to correct for the basis-set error of wave-function theory (WFT). One of the key ideas developed here is to define a range-separation parameter which automatically adapts to a given basis set. The derivation of the exact equations are based on the Levy-Lieb formulation of DFT, which helps us to define a complementary functional which corrects uniquely for the basis-set error of WFT. The coupling of DFT and WFT is done through the definition of a real-space representation of the electron-electron Coulomb operator projected in a one-particle basis set. Such an effective interaction has the particularity to coincide with the exact electron-electron interaction in the limit of a complete basis set, and to be finite at the electron-electron coalescence point when the basis set is incomplete. The non-diverging character of the effective interaction allows one to define a mapping with the long-range interaction used in the context of range-separated DFT and to design practical approximations for the unknown complementary functional. Here, a local-density approximation is proposed for both full-configuration-interaction (FCI) and selected configuration-interaction approaches. Our theory is numerically tested to compute total energies and ionization potentials for a series of atomic systems. The results clearly show that the DFT correction drastically improves the basis-set convergence of both the total energies and the energy differences. For instance, a sub kcal/mol accuracy is obtained from the aug-cc-pVTZ basis set with the method proposed here when an aug-cc-pV5Z basis set barely reaches such a level of accuracy at the near FCI level.
Chlorinated hydrocarbon compounds are of environmental concerns, since they are toxic to humans and other mammals, are widespread, and exposure is hard to avoid. Understanding and improving methods to reduce the amount of the substances is important. We present an atomic-scale calculational study of the adsorption of chlorine-based substance chloroform (CHCl3) on graphene oxide, as a step in estimating the capacity of graphene oxide for filtering out such substances, e.g., from drinking water. The calculations are based on density functional theory (DFT), and the recently developed consistent-exchange functional for the van der Waals density-functional method (vdW-DF-cx) is employed. We obtain values of the chloroform adsorption energy varying from roughly 0.2 to 0.4 eV per molecule. This is comparable to previously found results for chloroform adsorbed directly on clean graphene, using similar calculations. In a wet environment, like filters for drinking water, the graphene will not stay clean and will likely oxidize, and thus adsorption onto graphene oxide, rather than clean graphene, is a more relevant process to study.
We present a kinetic-energy density-functional theory and the corresponding kinetic-energy Kohn-Sham (keKS) scheme on a lattice and show that by including more observables explicitly in a density-functional approach already simple approximation strategies lead to very accurate results. Here we promote the kinetic-energy density to a fundamental variable along side the density and show for specific cases (analytically and numerically) that there is a one-to-one correspondence between the external pair of on-site potential and site-dependent hopping and the internal pair of density and kinetic-energy density. Based on this mapping we establish two unknown effective fields, the mean-field exchange-correlation potential and the mean-field exchange-correlation hopping, that force the keKS system to generate the same kinetic-energy density and density as the fully interacting one. We show, by a decomposition based on the equations of motions for the density and the kinetic-energy density, that we can construct simple orbital-dependent functionals that outperform the corresponding exact-exchange Kohn-Sham (KS) approximation of standard density-functional theory. We do so by considering the exact KS and keKS systems and compare the unknown correlation contributions as well as by comparing self-consistent calculations based on the mean-field exchange for the keKS and the exact-exchange for the KS system, respectively.
We report on the successful synthesis and hyperpolarization of N unprotected {alpha} amino acid ethyl acrylate esters and extensively, on an alanine derivative hyperpolarized by PHIP (4.4$pm$1% $^{13}$C-polarization), meeting required levels for in vivo detection. Using water as solvent increases biocompatibility and the absence of N-protection is expected to maintain biological activity.
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