The equivalent potential of water for electronic structure of aspartic acid

The equivalent potential of water for the electronic structure of aspartic acid (Asp(-)) in solution is constructed by the first-principles, all-electrons, ab initio calculations. Aspartic acid is a hydrophilic amino acid which is negatively charged in neutral water solution. The main process of calculation consists of three steps. Firstly, the geometric structure of the cluster containing Asp(-) and water molecules is calculated by the free cluster calculation. Then, based on the obtained geometric structure, the electronic structure of Asp(-) with the potential of water molecules is calculated using the self-consistent cluster-embedding method. Finally, the electronic structure of Asp(-) with the potential of dipoles is calculated. The results show that the major effect of water on Asp(-)'s electronic structure is lowering the occupied molecular orbitals by about 0.02 Ry on average, and narrowing energy gap by 10.8%. The effect of water on the electronic structure of Asp(-) can be simulated by dipoles potential.     

Investigations of the Properties of l-Histidine in Aqueous NaCl Solutions at Different Temperatures

Density and viscosity experimental data for l-histidine in NaCl aqueous solutions were obtained at different salt and different amino acid concentrations in the range of temperatures between 293.15 and 323.15 K. The results have been correlated and analyzed in order to evaluate the influence of electrolyte concentration and temperature on the volumetric and viscometric properties of the solutions. The apparent molar volumes and the transfer volumes of l-histidine in aqueous NaCl solutions at different salt and amino acid molalities over entire temperature range were calculated from experimental density data. The viscosity experimental data have been analyzed with Jones–Dole equation and the Falkenhagen (A) and the Jones–Dole coefficient (B) have been calculated in order to evaluate the interactions occurring in the systems. The B viscosity coefficients were found to be positive for all conditions, showing a kosmotropic effect of solutes, indicating an alignment of zwitterions with ions/water dipoles. A comparison of standard partial molar volumes for some amino acids in water and NaCl aqueous solutions shows that they increase with molecular mass and complexity of the lateral side chain of the amino acid.     

Equivalent potential of water molecules for electronic structure of glutamic acid

The fundamental importance of the electronic structure of molecules is widely recognized. To get reliable electronic structure of protein in aqueous solution, it is necessary to construct a simple, easy-use equivalent potential of water molecules for protein's electronic structure calculation. Here, the first-principles, all-electron, ab initio calculations have been performed to construct the equivalent potential of water molecules for the electronic structure of glutamic acid, which is a hydrophilic amino acid and is negatively charged (Glu(-)) in neutral water solution. The main process of calculation consists of three steps. Firstly, the geometric structure of the cluster containing Glu(-) and water molecules is calculated by free cluster calculation. Then, based on the geometric structure, the electronic structure of Glu(-) with the potential of water molecules is calculated using the self-consistent cluster-embedding method. Finally, the electronic structure of Glu(-) with the potential of dipoles is calculated. Our calculations show that the major effect of water molecules on Glu(-)'s electronic structure is lowering the occupied electronic states by about 0.017 Ry, and broadening energy gap by 12%. The effect of water molecules on the electronic structure of Glu(-) can be well simulated by dipoles potential.     

[3+2] Redox‐Neutral Cycloaddition of Nitrocyclopropanes with Styrenes by Visible‐Light Photocatalysis

The first nitro‐group‐initiated redox‐neutral [3+2] cycloaddition of nitrocyclopropanes with alkenes by using visible‐light‐absorbing transition‐metal complexes was reported. High diastereoselectivities were observed for two quaternary carbon centers on the ring and validated by DFT calculations. Spiro‐ or polycyclic structures can be constructed smoothly. Cyclic γ‐amino acid derivatives and polysubstituted cyclic amino alcohols can be obtained easily through reduction of the nitro group.     

Conformational study of charged cyclohexyldiamines and their gas phase acid–base properties

Quantum chemical calculations employing the MP2/aug-cc-pVDZ model chemistry have been used to investigate the structure of mono- and diprotonated forms of cyclohexyldiamine (CHDA) isomers. The strength of the intramolecular hydrogen bonds and ion–dipole interactions between the amino groups, which play a key role in the conformational behaviour of the monoprotonated forms, is estimated by isodesmic reactions and electrostatic calculations. The energy variations found for the diprotonated forms are explained by the electrostatic repulsions between the amino groups. From the Gibbs energies and enthalpies calculated for the neutral and protonated CHDAs, the gas-phase basicities and proton affinities of the neutral and monoprotonated forms were determined and discussed.     

Charge distribution and hydrogen bonding of a collagen α2‐chain in vacuum,hydrated, neutral,and charged structural models

A challenging task in computational biophysics is to ascertain the solvent effect on the electronic structure and interatomic bonding at the atomistic level. Simulations must be carried out on reasonably large biomolecules for accurate calculations to yield valid results. We report the results of a calculation on collagen model in the form of a peptide under three different environments: vacuum, solvated and with neutral and charged sites. Quantitative results and analysis of the partial charge (PC) distribution on each amino acid are discussed. A significant charge transfer of more than 1 electron from protein to water molecules is found with similar results when the model contains charged sites. The main contributions to the interatomic bonding are from hydrogen bonds (HBs) between water‐water and water‐protein pairs. A connection between PC and HBs can be established since the nonpolar amino acids form no HBs and have the smallest PC and vice versa. The ab initio PC obtained are used in the NAMD simulation showing significant improvement over the default values as reflected in the root mean square deviation of atomic positions in the MD steps and the total free energy in energy minimization. These results could facilitate the interpretation of data on interaction of various ligands in charged proteins in relation to isoelectric points. © 2016 Wiley Periodicals, Inc.     

A theoretical investigation of the relative stability of hydrated glycine and methylcarbamic acid--from water clusters to interstellar ices

We have theoretically investigated how the low-energy conformers of the neutral and the zwitterionic forms of glycine as well as methylcarbamic acid are stabilized by the presence water. The MP2/6-311++G(d,p) method was utilized to conduct calculations on glycine and methylcarbamic acid in both isolated clusters and in clusters embedded in the conductor-like polarizable continuum model (C-PCM), where the clusters explicitly contain between one and ten water molecules. The neutral forms of glycine and methylcarbamic acid were found to have similar hydration energies, whereas the neutral methylcarbamic acid was determined to be approximately 32 kJ mol(-1) more stable than the neutral glycine in the isolated clusters and 30 kJ mol(-1) more stable in the C-PCM embedded clusters. Both the number and strength of the hydrogen bonding interactions between water and the zwitterions drive the stability. This lowers the relative energy of the glycine zwitterion from 50 kJ mol(-1) above neutral glycine, when there are two water molecules in the clusters to 11 kJ mol(-1) below for the clusters containing ten water molecules. For the methylcarbamic acid clusters with two water molecules, the zwitterion is 51 kJ mol(-1) higher in energy than the neutral form, but it remains 13 kJ mol(-1) above the neutral methylcarbamic acid in the clusters containing ten water molecules. When the bulk water environment is simulated by the C-PCM calculations, we find both the methylcarbamic acid and glycine zwitterionic forms have similar energies at 20 kJ mol(-1) above the neutral methylcarbamic acid energy and 10 kJ mol(-1) lower than the neutral glycine energy. Although neither methylcarbamic acid nor glycine have been detected in the interstellar medium yet, our findings indicate that methylcarbamic acid is the more stable product from methylamine and carbon dioxide reactions in a water ice. This suggests that methylcarbamic acid likely plays a role in the intermediate steps if glycine is formed in the interstellar medium.     

Density functional theory reveals an increase in the amino 1H chemical shift in guanine due to hydrogen bonding with water

Electronic structure calculations underestimate the chemical shift of the non H-bonded amino proton 1H22 in isolated G-quartet structures. The current work shows that this underestimation is due to the absence of a water environment in the calculations: coordination of at least two water molecules is required to obtain good agreement with experiment. The results indicate how improved agreement between calculated and experimental (solution-phase) NMR data can be obtained.     

Vibrational spectrum of glycine molecule

The infrared and Raman spectra of glycine molecule has been studied in spectral region 400-4000 cm(-1) in solid form as well as in water. The vibrational frequencies for the fundamental modes of the glycine in neutral and its zwitterionic form have also been calculated using AM1 semiempirical method as well as ab initio method with minimal basis set. The reliability of the minimal basis set and AM1 method with higher basis sets, for IR spectra of the neutral glycine conformers were examined. We find that the 6-21G basis set calculation yields structural parameters, rotational constant and dipole moment of glycine conformers, which are very similar to those obtained from extended basis set calculation as well as experimental values. IR frequencies for glycine conformer I are also calculated in water using SCRF=PCM model and compared with experimental values. A comparison between calculated frequencies for neutral glycine, and its zwitterionic form with observed IR and Raman bands have been made. The total energies for gas phase glycine and its zwitterionic form along with those of hydrated forms were also calculated. It is found from the calculations that in the gas phase neutral glycine is more stable as compared to its zwitterionic form.     

Ionization of imidazole in the gas phase, microhydrated environments, and in aqueous solution

Hydration of neutral and cationic imidazole is studied by means of ab initio and molecular dynamics calculations, and by photoelectron spectroscopy of the neutral species in a liquid microjet. The calculations show the importance of long range solvent polarization and of the difference between the structure of water molecules in the first shell around the neutral vs cationic species for determining vertical and adiabatic ionization potentials. The vertical ionization potential of neutral imidazole of 8.06 eV calculated using a nonequilibrium polarizable continuum model agrees well with the value of 8.26 eV obtained experimentally for an aqueous solution at pH 10.6.     

Glycine Dimers: Structure,Stability, and Medium Effects

We report a study on different ionization states and conformations of the bimolecular (Gly)₂ system by means of quantum mechanical calculations. Optimized geometries for energy minima of the glycine dimer, as well as relative energies and free energies were computed as a function of the medium: gas phase, nonpolar polarizable solvent, and aqueous solution. The polarizable continuum model was employed to account for solvation effects. Energy calculations were done using the MP2/aug‐cc‐pVTZ and B3LYP/6‐311+G(2df,2p) methods on B3LYP/6‐31+G(d,p) optimized structures (some single‐point energy calculations were also done using the B3PW91 and PBE1KCIS methods). Ionized forms of the glycine dimer (either zwitterion–zwitterion or neutral–zwitterion) are predicted to exist in all media, in contrast to amino acid monomers. In aqueous solution, dimerization is an exergonic process (?4 kcal mol^?1). Thus, according to our results, zwitterion–zwitterion Gly dimers might be abundant in supersaturated glycine aqueous solutions, a fact that has been connected with the structure of α‐glycine crystals but that remains controversial in the literature. Another noticeable result is that zwitterion–zwitterion interactions are substantially underestimated when computed using methods based on density functional theory. For comparison, some calculations for the dimer of the simplest chiral amino acid alanine were done as well and differences to the glycine dimer are discussed.     

Comparative study of imidazole hydration: Ab initio and electrostatic calculations vs. Cambridge structural database analysis

We studied geometries and energies of complexes between water and neutral or protonated imidazole by ab initio molecular orbital calculations using the 4-31G basis set with and without the counterpoise correction. Positions of hydration sites and relative binding energies could be also estimated by using the electrostatic field map of imidazole as calculated by our bond increment method. The reliability of the calculations is confirmed by comparing the geometries of the imidazole-water complex to the experimental ones from the Cambridge Structural Database. These were obtained by X-ray diffraction studies on crystals with water bound to a molecule containing the imidazole fragment.     

Deprotonation sites of acetohydroxamic acid isomers. A theoretical and experimental study

Theoretical (ab initio calculations) and experimental (NMR, spectrophotometric, and potentiometric measurements) investigations of the isomers of acetohydroxamic acid (AHA) and their deprotonation processes have been performed. Calculations with the Gaussian 98 package, refined at the MP2(FC)/AUG-cc-pVDZ level considering the molecule isolated, indicate that the Z(cis) amide is the most stable form of the neutral molecule. This species and the less stable (Z)-imide form undergo deprotonation, giving rise to two stable anions. Upon deprotonation, the E(trans) forms give three stable anions. The ab initio calculations were performed in solution as well, regarding water as a continuous dielectric; on the basis of the relative energies of the most stable anion and neutral forms, calculated with MP2/PCM/AUG-cc-pVDZ, N-deprotonation of the amide (Z or E) structure appeared to be the most likely process in solution. NMR measurements provided evidence for the existence of (Z)- and (E)-isomers of both the neutral and anion forms in solution. Comparisons of the dynamic NMR and NOESY (one-dimensional) results obtained for the neutral species and their anions were consistent with N-deprotonation, which occurred preferentially to O-deprotonation. The (microscopic) acid dissociation constants of the two isomers determined at 25 degrees C from the pH dependence of the relevant chemical shifts, pK(E) = 9.01 and pK(Z) = 9.35, were consistent with the spectrophotometric and potentiometric evaluations (pK(HA) = 9.31).     

Matrix-isolation FT-IR spectroscopic study and theoretical DFT(B3LYP)/6-31++G** calculations of the vibrational and conformational properties of tyrosine

The complicated conformational isomerism of tyrosine is studied by experimental matrix-isolation FT-IR spectroscopy combined with theoretical DFT(B3LYP)/6-31++G** calculations. Not less than 18 possible conformations of tyrosine have been considered theoretically. The results revealed that the most and the less stable forms of neutral tyrosine have the same conformation of the main part of amino acid (conformation II) but they differ in orientation of the phenyl ring. The calculated values of the relative energies suggest that all conformations would be detectable in the experimental spectrum. However, it appeared that it is not possible to distinguish in the experimental spectrum between the bands due to the forms with the same conformation of the main part of amino acid but a different orientation of the phenol ring.     

Fractionation of peptide with disulfide bond for quantum mechanical calculation of interaction energy with molecules

We present a computational study of a recently developed molecular fractionation with conjugated caps (MFCC) method for application to peptide/protein that has disulfide bonds. Specifically, we employ the MFCC approach to generate peptide fragments in which a disulfide bond is cut and a pair of conjugated caps are inserted. The method is tested on two peptides interacting with a water molecule. The first is a dipeptide consisting of two cysteines (Cys-Cys) connected by a disulfide bond and the second is a seven amino acid peptide consisting of Gly-Cys-Gly-Gly-Gly-Cys-Gly with a disulfide cross link. One-dimensional peptide-water potential curves are computed using the MFCC method at various ab initio levels for a number of interaction geometries. The calculated interaction energies are found to be in excellent agreement with the results obtained from the corresponding full system ab initio calculations for both peptide/water systems. The current study provides further numerical support for the accuracy of the MFCC method in full quantum mechanical calculation of protein/peptide that contains disulfide bonds.     

Photoionization,Structures, and Energetics of Na-Doped Formic Acid–Water Clusters

The influence of formic acid on water cluster aggregation has been investigated experimentally by mass spectrometry and tunable UV laser ionization applied to Na-doped clusters formed in the supersonic expansion of water vapors seeded with formic acid (FA) as well as theoretically using high level quantum chemistry methods. The mass spectra of Na−FA(H₂O)_n clusters show an enlarging of mass distribution toward heavier clusters with respect to the Na−(H₂O)_n clusters, suggesting similar mass distribution in neutral clusters and an influence of formic acid in water aggregation. Density functional theory and coupled-cluster type (DLPNO-CCSD(T)) calculations have been used to calculate structures and energetics of neutral and ionized Na−FA(H₂O)_n as well as neutral FA(H₂O)_n. Na-doped clusters are characterized by very stable geometries. The theoretical adiabatic ionization potential values match pretty well the measured appearance energies and the calculated first six electronic excited states show Rydberg-type characters, indicating possible autoionization contributions in the mass spectra. Finally, theoretical calculations on neutral FA(H₂O)_n clusters show the possibility of similarly stable structures in small clusters containing up to n=4–5 water molecules, where FA interacts significantly with waters. This suggests that FA can compete with water molecules in the starting stage of the aggregation process, by forming stable nucleation seed.     

Polysaccharide‐templated twisted assemble of 2‐anilinonaphthalene‐6‐sulfonic acid

Schizophyllan (SPG) is a natural β‐1,3‐glucan that forms a triple helix (t‐SPG) in neutral aqueous solutions and t‐SPG can be denatured to single chains (s‐SPGs) in DMSO or alkaline solutions. Exchanging the denatured solutions for neutral water leads the renaturation of the triple helix. We have reported that hydrophobic molecules can form a complex with s‐SPG when they are present in the renaturation process. Some of these, for example poly(dA) and polyaniline, were found to have aromatic amino moieties. This report demonstrates whether s‐SPG can interact with other aromatic amino compounds such as anilinonaphthalene sulfonic acid (ANS) derivatives. Enhanced fluorescence intensity and red‐shifted UV absorption spectra were observed in the mixture of s‐SPG and 2,6‐ANS or 2,6‐TNS. In the circular dichroism measurement, the positive Cotton effects appeared after mixing 2, 6‐ANS with s‐SPG. When the amino proton was replaced by the methyl group or used in intramolecular hydrogen bonds, any spectral changes were not observed. These results indicate that amino proton in the ANS derivatives plays a key role in the complexation. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 1440–1448, 2008     

Calculation of the water-cyclohexane transfer free energies of neutral amino acid side-chain analogs using the OPLS all-atom force field

We calculated the free energy of solvation of the neutral analogs of 18 amino acid side-chains (not including glycine and proline) using the OPLS all-atom force field in TIP4P water, SPC water, and cyclohexane by molecular dynamics simulation and thermodynamic integration. The average unsigned errors in the free energies of solvation in TIP4P, SPC, and cyclohexane are 4.4, 4.9, and 2.1 kJ/mol respectively. Most of the calculated hydration free energies are not favorable enough compared to experiment. The largest errors are found for tryptophan, histidine, glutamic acid, and glutamine. The average unsigned errors in the free energy of transfer from TIP4P to cyclohexane and from SPC to cyclohexane are 4.0 and 4.1 kJ/mol, respectively. The largest errors, of more than 7.5 kJ/mol, are found for histidine, glutamine, and glutamatic acid.     

A theoretical study of structures and electron affinities of radical anions of guanine-cytosine, adenine-thymine, and hypoxanthine-cytosine base pairs

Adiabatic electron affinities (AEA) and structural perturbations due to addition of an excess electron to each of the neutral guanine-cytosine (G-C), adenine-thymine (A-T), and hypoxanthine-cytosine (HX-C) base pairs were studied using the self-consistent charge, density functional tight-binding (SCC-DFTB-D) method, augmented by the empirical London dispersion energy term. Performance of the SCC-DFTB-D method was examined by comparing the calculated results using it with those obtained from experiment as well as ab initio and other different density functional theoretical studies. An excellent agreement between the SCC-DFTB-D results and those obtained by the other calculations regarding the structural modifications, hydrogen bonding, and dissociation energies of the neutral and radical anion base pairs was found. It is shown that adiabatic electron affinity can be better predicted by considering reaction enthalpies of formation of the respective neutral and anionic base pairs from their respective molecular components instead of taking the difference between their total energies. The calculated AEAs of the base pairs were compared with those obtained by the bracketing method from Schaefer and coworkers, where a satisfactory agreement was found. It shows applicability of the SCC-DFTB-D method to study charged DNA models at a highly economical computational cost.     

Solvation free energy of amino acids and side-chain analogues

The solvation free energies of amino acids and their side-chain analogues in water and cyclohexane are calculated by using Monte Carlo simulation. The molecular interactions are described by the OPLS-AA force field for the amino acids and the TIP4P model for water, and the free energies are determined by using the Bennett acceptance method. Results for the side-chain analogues in cyclohexane and in water are used to evaluate the performance of the force field for the van der Waals and the electrostatic interactions, respectively. Comparison of the calculated hydration free energies for the amino acid analogues and the full amino acids allows assessment of the additivity of the side chain contributions on the number of hydrating water molecules. The hydration free energies of neutral amino acids can be reasonably approximated by adding the contributions of their side chains to that of the hydration of glycine. However, significant nonadditivity in the free energy is found for the zwitterionic form of amino acids with polar side chains. In serine and threonine, intramolecular hydrogen bonds are formed between the polar side chains and backbone groups, leading to weaker solvation than for glycine. In contrast, such nonadditivity is not observed in tyrosine, in which the hydroxyl group is farther separated from, and therefore cannot form an intramolecular hydrogen bond with, the backbone. For histidine we find that a water molecule can form a bridge when the intramolecular hydrogen bond between the polar group and the backbone is broken.