Conformational search for zwitterionic leucine and hydrated conformers of both the canonical and zwitterionic leucine using the DFT-CPCM model

The stable conformations for zwitterionic leucine have been searched for in solution as well as in gas phase. A total of 54 trial structures were generated by considering possible combinations of single bond rotamers. It is observed that zwitterions are not stable in gas phase. In order to investigate the zwitterions of leucine in solution, the calculations for all trial structures of zwitterions were performed initially at the PM3 level and 14 the lowest energy structures were reoptimized at the B3LYP/6-311G(d) level using the CPCM model. Seven of these conformers of zwitterionic leucine were found to be stable in solution. The five most stable conformers were then reoptimized at the B3LYP/6-311++G(d, p) level. The energy ordering of the canonical leucine(neutral) conformers were also considered on the basis of single point energy calculations at the B3LYP/6-311++G(d, p) level using the CPCM model. The chemical hardness, chemical potential, vertical ionization energy and vertical electron affinity were calculated for a few of the most stable canonical leucine and its zwitterions in solution. The effects of explicit addition of water molecules (microsolvation) on the structure and the energy of both canonical and zwitterionic conformers of leucine were investigated. It is noted that in gas phase, the singly and doubly hydrated canonical (neutral) forms are more stable than their zwitterionic counterparts. The solvated zwitterions and canonical structures of leucine were further investigated using the discrete/SCRF model with zero, one and two water molecules. In solution, the continuum solvent model shows that the bare zwitterionic form is more stable than the bare canonical form by 1.6 kcal/mol. This energy separation is increased to 3.8 and 4.8 kcal/mol with inclusion of one and two water molecules, respectively. The optimized structural parameters for the most stable zwitterionic leucine with zero, one and two water molecules in solution were compared with those reported for l-leucine crystal, which shows a close agreement between the optimized geometrical parameters of the zwitterionic leucine with two water molecules in solution with the experimental geometrical parameters for l-leucine crystal. It is also observed that when the structures of zwitterions with one and two explicit water molecules are optimized in solution, the geometrical parameters and their relative energies are found to be appreciably modified. We have also calculated the vibrational spectra of the most stable solvated zwitterionic leucine as well as for the most stable structure of zwitterionic leucine with one and two water molecules in solution.     

Analysis of the structures,energetics, and vibrational frequencies for the hydrogen-bonded interaction of nucleic acid bases with Carmustine pharmaceutical agent: a detailed computational approach

In the present study, it is attempted to scrutinize the hydrogen bonding interaction between Carmustine drug and DNA pyrimidine bases by means of density functional theory calculations regarding their geometries, binding energies, vibrational frequencies, and topological features of the electron density in the gas phase and the water solution. Based on the density functional theory results, it is found that the process of intermolecular interaction between Carmustine drug and nucleobases is exothermic and all of the optimized configurations are stable. Furthermore, the negative stability energy represented by a polarizable continuum model shows the significant increase in the solubility of the nucleobase after hydrogen bonding intermolecular interaction in the presence of water solvent. It is also found that the intermolecular hydrogen bonds between drug and the nucleobases play the significant role in the stability of the physisorption configurations. Hydrogen bond energies for hydrogen-bonded complexes are obtained from Espinosa method and the atoms-in-molecules theory are also applied to get a more precise insight into the nature of the intermolecular hydrogen bond interactions.     

Charge calculations in molecular mechanics. III: Amino acids and peptides

Atomic charges obtained with a previously published charge scheme are given for amino acids and peptides. In order to do this, a method of handling charged species with the basic scheme^2,3 has been developed. The charges obtained for alkylammonium ions and carboxylate ions with the scheme are presented and compared with CNDO and ab initio values. The calculated experimental dipole moments of the zwitterionic forms of glycine, alanine and β-alanine are then discussed. Finally, the atomic charges obtained for the naturally occurring amino acids are given, both in the form of the N-acetyl-N′-methyl amino acid amides, used as models for the amino acid residues in enzymes, and as the free zwitterionic amino acids. The charges obtained show a good correlation with n. m. r. chemical shifts of both carbon and hydrogen atoms.     

Ab initio molecular dynamics free-energy study of microhydration effects on the neutral-zwitterion equilibrium of phenylalanine.

The structures and relative energies of the most stable conformers of both naked and microsolvated phenylalanine, Phe.(H(2)O)(n)(n=0-3), are calculated by density functional theory. For selected structures, coordination-constrained ab initio molecular dynamics simulations determine the proton-transfer mechanism connecting neutral and zwitterionic forms of Phe. The associated free-energy profiles are calculated by thermodynamic integration. While no zwitterionic free-energy minimum is found for naked Phe, microsolvation is found to stabilize the zwitterionic form. For cluster sizes n > or = 3, the proton-transfer equilibrium shifts towards the zwitterionic structure for specific proton-transfer pathways. The energetically most favourable interconversion path between the neutral and zwitterionic forms is through a H(2)O bridge with free-energy barriers as low as 14.4 kJ mol(-1) for Phe.(H(2)O)(3). The free energy required for breaking a carboxylic OH bond involved in intramolecular hydrogen bonding is typically lower than in the water-assisted case. However, the resulting zwitterion turns out to be unstable with respect to the backward proton-transfer reaction.     

Stabilization of zwitterions in solution: phosphinic and phosphonic acid GABA analogues

The influence of treatment of electron correlation, size of basis set and choice of solvation model on the predicted stabilization of zwitterionic phosphinic and phosphonic acid gamma-aminobutyric acid (GABA) analogues is investigated using ab initio molecular orbital methods and density functional theory. Density functional theory with the B3LYP functional and a composite basis set composed of the 6-31+G(2df) basis for phosphorus atoms and the 6-31+G(d,p) basis set for all other atoms is found to give an acceptable tradeoff between accuracy and computational expense. Either directly optimizing zwitterionic conformers within the conductor-like screening solvation model (COSMO) or pre-optimizing as dihydrates and then applying the COSMO solvation model give an acceptable treatment of solvation in terms of determining stable solvated structures, although directly optimizing within COSMO is simpler and less computationally expensive. With this protocol, cis-constrained phosphinic and phosphonic acid GABA analogues, which exhibit lower affinities for GABAC receptors, are found to possess only folded, intramolecularly hydrogen bonded low energy conformers. Trans-constrained analogues, on the other hand, exhibit higher affinities for GABAC receptors and are found to exist only as partially folded stable conformers. Conformationally flexible analogues can attain folded, partially folded or fully extended conformations and also have high biological activity. These results imply that the partially folded conformation is likely to be the most biologically active.     

Density functional theory and atoms-in-molecules investigation of intramolecular hydrogen bonding in derivatives of malonaldehyde and implications for resonance-assisted hydrogen bonding

A density functional theory (DFT) and atoms-in-molecules (AIM) analysis has been applied to the intramolecular hydrogen bonding in the enol conformers of malonaldehyde and its fluoro-, chloro-, cyano-, and nitro-substituted derivatives. With the B3LYP/6-311++G(2d,p) method, good agreement between the DFT geometries and published experimental structures has been found. The donor-acceptor distance was also varied in a series of constrained optimizations in order to determine if energetic, structural, and topological trends associated with intermolecular hydrogen bonding remain valid in the intramolecular case. At very short donor-acceptor distances (<2.24 A), the hydrogen is symmetrically located between donor and acceptor; at distances longer than this, the hydrogen bonding is no longer symmetric. The AIM methodology has been applied to explore the topology of the electron density in the intramolecular hydrogen bonds of the chosen model systems. Most AIM properties for intramolecular hydrogen bond distances longer than 2.24 A show smooth trends, consistent with intermolecular hydrogen bonds. Integrated AIM properties have also been used to explore the phenomenon of resonance-assisted hydrogen bonding (RAHB). It is shown that as the donor-acceptor distance is varied, pi-electron density is redistributed among the carbon atoms in the intramolecular hydrogen bond ring; however, contrary to prior studies, the integrated atomic charges on the donor-acceptor atoms were found to be insensitive to variation of hydrogen-bonding distance.     

Sum frequency vibrational spectroscopy of leucine molecules adsorbed at air-water interface

Sum frequency vibrational spectroscopy was used to study adsorption of leucine molecules at air-water interface from solutions with different concentrations and pH values. The surface density and the orientation of the isopropyl head group of the adsorbed leucine molecules could be deduced from the measurements. It was found that the orientation depends on the surface density, but only weakly on bulk pH value at the saturated surface density. The vibrational spectra of the interfacial water molecules appeared to be strongly affected by the charge state of the adsorbed leucine molecules. Enhancement and inversion of polar orientation of interfacial water molecules by surface charges or field controllable by the bulk pH value were observed.     

Separation of inorganic anions using a series of sulfobetaine exchangers

A set of five new sulfobetaine exchangers with inner quaternary amines and outer sulfonic acids have been prepared. A series of zwitterionic precursors was attached to highly porous divinylbenzene polymer using a grafting reaction, which allows a flexible adjustment of the degree of functionalisation. The resulting materials have identical spacers to the polymeric backbone and differ only in chain length between the charged functional groups. Capacities of the stationary phases were analysed by two different methods based on elemental analysis and the results obtained were found to correlate. The application of combustion elemental analysis proved an identical molar content of sulfur and nitrogen. The distance between the charged functional groups is varied from one to five methylene groups for a better understanding of the retention behaviour of inorganic anions on zwitterionic stationary phases. Inorganic anions were separated using sodium acetate eluents with varying ionic strength and pH and the behaviour of all columns has been compared to each other and to ZIC-HILIC and ZIC-pHILIC columns from Merck SeQuant. The exchangers with two and five methylene groups between the charges showed the highest retention factors. Polarity and accessibility of the anion exchange sites are dependent on the distance between the charged groups and the flexibility of the chains. These properties have a strong influence on anion separations. The exchanger with two methylene groups between the charged functional groups showed the biggest difference as compared to the commercially available ZIC-HILIC and ZIC-pHILIC exchangers.     

Separation of -amino acids using a series of zwitterionic sulfobetaine exchangers

A set of five new covalently bond sulfobetaine exchangers with inner quaternary amines and outer sulfonic acids have been prepared by attachment of a series of zwitterionic precursors to hyperporous divinylbenzene polymers using a grafting reaction. The series of zwitterionic exchangers have the same backbone and identical spacers to the polymeric backbone, as well as comparable capacities. The only difference is the chain length for one to five methylene groups between the charged functional groups. Chromatographic properties are examined by separation of α-amino acids using sodium acetate and nitric acid eluents. The separation mechanism is explored by varying eluent ionic strength and eluent pH, resulting in the conclusion that amino acids are separated due to cation exchange interactions. This is a behavior never before observed using zwitterionic exchangers. It contradicts the fact that sulfobetaine-type materials used in zwitterionic ion chromatography (ZIC) usually are well suited for anion separation and only poorly for cation separation. Contrary to anion separations using the identical set of exchangers, the materials with three and four methylene groups between the charges give the highest retention factors. Materials showing the high potential in ZIC separations of inorganic anions give low retention factors for amino acids and vice versa.     

SDS对SB3-12胶束表面电荷密度的调控作用及对药物增溶的影响

两性离子甜菜碱表面活性剂(SB3-12)胶束具有较好的生物相容性,由于相反电荷的极性头之间具有静电中和作用,胶束表面具有小的负电荷密度。当加入阴离子的十二烷基硫酸钠(SDS)以后,负离子SD-与SB3-12胶束极性区内层季铵正电荷的静电中和作用,能连续地调节胶束表面磺酸基的负电荷密度,这有利于对药物分子的选择性增溶和调节在生理条件下的药物的输送。等温滴定量热(ITC)研究发现SB3-12和SDS有强的协同效应,混合临界胶束浓度(CMC)和胶束化焓明显降低,并得到两者协同效应的弱静电作用机理。当模型药物分子芦丁(Rutin)与SB3-12/SDS混合胶束作用时,芦丁7位羟基的氢解离后的阴离子与SDS共同作用于SB3-12形成混合胶束。UV-Vis吸收光谱和~1H NMR谱研究发现,在SB3-12胶束中,芦丁分子的A环位于季铵阳离子附近,B环位于两个相反电荷之间的弱极性区域。在SDS胶束中,B环位于栅栏层,而A环和二糖暴露于水相侧。在混合胶束中,随着SDS摩尔分数增加,对A环的静电吸引变弱。离子表面活性剂对两性离子表面活性剂胶束表面电荷密度的调节作用,本质上是对胶束极性区域的物理及化学性质的微调,进而实现对药物的可控增溶。     

对体系局部进行高精度量子化学计算的研究

用对大体系的局部区域进行高精度量子化学计算的新方法，对腈、酰胺、醚、醛、羧酸、硝基化合物、卤代物等不同类型的多种有机分子体系进行计算，得到电荷分布、键断裂能、电离势与电负性等方面的数据.为了比较，同时对上述体系进行整体的和模型体系的高精度计算.局部高精度计算与整体高精度计算的结果相当一致，优于模型体系的计算结果，进一步表明了局部高精度量子化学计算方法的可行性.     

Experimental/theoretical electrostatic properties of a styrylquinoline-type HIV-1 integrase inhibitor and its progenitors

We have established that polyhydroxylated styrylquinolines are potent inhibitors of HIV-1 integrase (IN). Among them, we have identified (E)-8-hydroxy-2-[2-(4,5-dihydroxy-3-methoxyphenyl)-ethenyl]-7-quinolinecarboxylic acid (1) as a promising lead. Previous molecular dynamics simulations and docking procedures have shown that the inhibitory activity involves one or two metal cations (Mg2+), which are present in the vicinity of the active center of the enzyme. However, such methods are generally based on a force-field approach and still remain not as reliable as ab initio calculations with extended basis sets on the whole system. To go further in this area, the aim of the present study was to evaluate the predictive ability of the electron density and electrostatic properties in the structure-activity relationships of this class of HIV-1 antiviral drugs. The electron properties of the two chemical progenitors of 1 were derived from both high-resolution X-ray diffraction experiments and ab initio calculations. The twinning phenomenon and solvent disorder were observed during the crystal structure determination of 1. Molecule 1 exhibits a planar s-trans conformation, and a zwitterionic form in the crystalline state is obtained. This geometry was used for ab initio calculations, which were performed to characterize the electronic properties of 1. The electron densities, electrostatic potentials, and atomic charges of 1 and its progenitors are here compared and analyzed. The experimental and theoretical deformation density bond peaks are very comparable for the two progenitors. However, the experimental electrostatic potential is strongly affected by the crystal field and cannot straightforwardly be used as a predictive index. The weak difference in the theoretical electron densities between 1 and its progenitors reveals that each component of 1 conserves its intrinsic properties, an assumption reinforced by a 13C NMR study. This is also shown through an excellent correlation of the atomic charges for the common fragments. The electrostatic potential minima in zwitterionic and nonzwitterionic forms of 1 are discussed in relation with the localization of possible metal chelation sites.     

Intermolecular-medium and intramolecular-weak hydrogen bonding chains in the crystals of chiral trifluoromethylated amino alcohols

A structural feature of hydrogen bonding chains found in the crystals of trifluoromethylated amino alcohols is reported. Hydrogen bondings of 3-(N,N-dialkylamino)-1,1,1-trifluoro-2-propanols construct chiral spiral hydrogen bonding chains. Lone pairs on the nitrogen atoms of the amino alcohols participate in two hydrogen bondings. Detailed structural analysis of the hydrogen bonds of the 3-(N,N-dimethylamino)-1,1,1-trifluoro-2-propanol suggested that the chain built up with alternating intermolecular-medium and intramolecular-weak hydrogen bonds. The medium intermolecular hydrogen bond, which transfers a proton from the hydroxy group to the amino nitrogen, would make a tentative zwitterionic form of the molecule. Then, electrostatic attraction between the charges in the zwitterion centers induced a weak intramolecular hydrogen bond.     

Effect of end groups of poly(n-butyl methacrylate) on its biocompatibility

Telechelic poly(n-butyl methacrylate)s (PBMAs) with various end groups were prepared using nonionic, anionic, cationic or zwitterionic azo-type radical initiators and cell adhesion onto the surfaces of the polymers was investigated. The tendency for cell adhesion to the polymers differed with and without pretreatment with phosphate-buffered saline (PBS, pH 7.4). The cell adhesion to polymer surfaces without pretreatment was lower than that with pretreatment. The effect of pretreatment with PBS was significant for PBMA with ionic end groups. Furthermore, cell adhesion to the surface of PBMA with zwitterionic end groups was suppressed compared with that to the surfaces of other polymers. It was presumed that positive and negative charges of zwitterionic groups in the same molecule negated each other at pH 7.4 and that the polymers with zwitterionic end groups had no effective charges. The results clearly indicated that biocompatibility of polymers can be changed by the introduction of functional groups at the ends of the polymer chains. Fabrication of functional material surfaces will be anticipated by the similar method in the future.     

Theoretical study of the gas-phase structures of sodiated and cesiated leucine and isoleucine: zwitterionic structure disfavored in kinetic method experiments

The most stable charge-solvated (CS) and zwitterionic (ZW) structures of sodiated and cesiated leucine and isoleucine were studied by density functional theory methods. According to the Boltzmann distribution in gas phase, both forms of LeuNa+ and IleNa+ exist, but in LeuCs+ and IleCs+, the ZW forms are dominant. Results for the sodiated compounds are consistent with the relationship found between decrease in relative stability of CS versus ZW form and aliphatic amino acid side chain length. The observed degeneracy in energy for IleNa+ conformers is at odds with kinetic method results. Additional calculations showed that kinetic method structural determinations for IleNa+ do not reflect relative order of populations in the lowest energy conformers. Since complexation of cationized amino acids into ion-bound dimers disfavors ZW structure by approximately 8 kJ mol(-1), it is suggested that for energy close conformers of sodium-cationized amino acids, the kinetic method may not be reliable for structural determinations.     

Properties of atoms in molecules

Atomic charges calculated by the population analysis method for three types of semi-empirical wave functions have been compared with charges obtained by integrating the corresponding electronic density functions over individual atomic regions. It was found that the two sets of charges compare quite well for CNDO wave functions and for extended-Hückel functions which are in terms of orthogonalized basis orbitals. However only the CNDO charges are reasonably close to those obtained by integrating near-Hartree-Fock electronic density functions.     

Direct Visual Evidence for Neutral and Charged Hexaphyrin Aromaticity with and without Keto-Defect

We use density functional theory and time-dependent together with a set of extensive mul-tidimensional visualization techniques to characterize the influence of keto effect on charge distribution at ground state and electronic transitions for neutral and charged hexaphyrin aromaticity with and without keto-defect. It is found that the aromaticity is the key fac-tor to influence the ground state Mulliken charges distribution properties, other than the meso-aryl-substituted effect. But with the enhancement of the keto-defect, the distributionchanges of Mulliken charges on the hexaphyrin groups are larger than those on the pentaflu-orophenyl substituted groups, following with the aromaticity changes from nonaromatic toaromatic. Furthermore, through characterizing by transition density and charge difference density, direct visual evidence for neutral and charged aromaticity with and without keto-defect can be clearly derived, and the ability of charge transfer between units of monoradical (nonaromaticity) and singlet biradical (aromaticity) forms is much stronger than that of neutral forms.     

Zwitterionic surfactants in ion binding and catalysis

Zwitterionic surfactants have unique properties for applications in separation methods and catalysis. Their properties and efficiencies depend on two main factors: surfactant structure and preferential interactions of zwitterionic surfactant interfaces with anions. Structural changes are related to hydrocarbon chain length, distance between charges, and type and order of functional groups in the polar head. Interactions of anions with zwitterionic micelles follow the Hofmeister series and change the surface charge. The interactions between surfactants and molecules/ions allow the rational control of separation by chromatography and micellar capillary electrophoresis; cloud point extraction; and stabilization and catalytic activity of biomolecules and nanoparticles.     

Multipole correction of atomic monopole models of molecular charge distribution. I. Peptides

The defects in atomic monopole models of molecular charge distribution have been analyzed for several model-blocked peptides and compared with accurate quantum chemical values. The results indicate that the angular characteristics of the molecular electrostatic potential around functional groups capable of forming hydrogen bonds can be considerably distorted within various models relying upon isotropic atomic charges only. It is shown that these defects can be corrected by augmenting the atomic point charge models by cumulative atomic multipole moments (CAMMs). Alternatively, sets of off-center atomic point charges could be automatically derived from respective multipoles, providing approximately equivalent corrections. For the first time, correlated atomic multipoles have been calculated for N-acetyl, N'-methylamide-blocked derivatives of glycine, alanine, cysteine, threonine, leucine, lysine, and serine using the MP2 method. The role of the correlation effects in the peptide molecular charge distribution are discussed.