Viscosimetric studies on molecular weight fractions of fulvic and humic acids of aquatic,terrestrial and microbial origin

Summary Viscosities were investigated of solutions of fulvic and humic acid molecular weight fractions of aquatic, terrestrial and microbial origin. Aquatic fulvic and humic acid molecules were, at pH 7, more voluminous than other types of humic compounds of similar molecular weight. It would appear that in low molecular weight non-aquatic humic matter, more inter- than intra-molecular bonding is present, with increasing molecular weight the bonding becomes more intra-molecular. Differences between average molecular weight values as obtained by an ultrafiltration method (Amicon) and by viscosimetry ranged from –18.7 to 18.5%. The largest deviations were in the low molecular weight range (<5,500 daltons). Higher molecular weight humics (in particular humic acids) appeared to have a more elongated structure than lower molecular weight material (in particular fulvic acids). Indications were obtained that on hydration humic moleculars become more elongated.     

Chemical and structural evolution of humic acids during organic waste composting

The effects of the composting process on the chemical and structural properties of humic acids have been studied in seven different organic waste mixtures from different origin. Only slight changes in elemental composition have been found in the humic acids after the composting process pointing to a more aromatic structure with higher proportions of oxygen and nitrogen. Functional groups were the most sensitive to the changes caused by the composting process showing a marked increase in the total acidity and phenolic, carboxyl and carbonyl groups. Gel permeation chromatography showed a slight increase in the average molecular weight of the humic acids. Infrared spectroscopy did not show important differences in humic acid structure but a clear decrease in the intensity of the bands in the region 3000–2850 cm^-1 corresponding to the aliphatic fractions. As a general result, the composting process yields humic acids in which the elemental and functional composition are closer to that of the more humified soil humic acids.     

Stability of Ca2+-, Cd2+-, Cu2+-[illite-humic] complexes and pH influence

Decomposition of fresh plant residues in soil is expected to produce humic fractions varying in molecular size. It was hypothesized that metal adsorption by soil, to some degree, will depend on humic acid content and molecular size. The latter is expected to vary in number and type of functional groups. In this study, illite-humic complexes were used to evaluate Ca²⁺, Cd²⁺, and Cu²⁺ adsorption and how this adsorption was affected by humic acids, differing in molecular size, under various pH values. Potentiometric titration using ion-selective electrodes with a stop-and-go procedure was employed to evaluate metal-[illite-humic] complex formation. The results showed that illite-humic complexes exhibited at least two types of metal-ion adsorption sites (low and high affinity) and molecular size of humic fractions had a large potential influence on total metal adsorption but a relatively smaller influence on metal-complex stability. Relative strength of metal-ion-[illite-humic] complexes followed the order of Cu²⁺>Cd²⁺>Ca²⁺ and were affected by pH, especially for low metal-ion affinity sites. Magnitude of metal-[illite-humic] stability constants, depending on molecular size of humic fraction and pH, varied on a log-scale from 3.52 to 4.21 for Ca²⁺, 4.38 to 5.18 for Cd²⁺and from 5.23 to 5.83 for Cu²⁺. There was an approximate 5-fold difference in these stability constants between the three different sizes of humic fractions. The larger the humic fraction, the lower the metal-[illite-humic] stability constant. This revised version was published online in June 2006 with corrections to the Cover Date. This revised version was published online in June 2006 with corrections to the Cover Date. This revised version was published online in June 2006 with corrections to the Cover Date.     

Theoretical study of antagonists and inhibitors of mammalian adenosine deaminase. II. Isomeric aza-deazaanalogues of adenosine

Isomeric aza-deazaanalogues of adenosine and their N1-protonated forms (except for that of 8-aza-1-deazaadenosine) were studied by computer modeling to find a relationship between their molecular structures and the properties as substrates for the mammalian adenosine deaminase. The atomic charge distribution and maps of the electrostatic potential around their van der Waals molecular surface were calculated using the ab initio STO-3G method. The conformational studies were carried out by the MM+ method of molecular mechanics. The previously proposed mechanism of the substrate acceptance in the active site of mammalian adenosine deaminase was refined, and the potential substrate properties were predicted for two previously unstudied adenosine analogues, 5-aza-9-deazaadenosine and 8-aza-3-deazaadenosine.     

Theoretical study of antagonists and inhibitors of mammalian adenosine deaminase. I. Adenosine and its aza- and deaza-analogs

Aza- and deazaanalogues of adenosine, including their 1-protonated forms (except for that of 1-deazaadenosine), were studied by computer computation to find a relationship between their molecular structures and substrate properties for the mammalian adenosine deaminase. The atomic charge distribution and maps of the electrostatic potential around their van der Waals molecular surface were calculated for these compounds using the ab initio STO-3G method. The conformational studies were carried out by the MM+ method of molecular mechanics. The mechanism that determines the substrate selectivity of mammalian adenosine deaminase is discussed. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2002, vol. 28, no. 4; see also http://www.maik.ru.     

Roles of Soil Organic Matter and Humic Substance Structure in Cu and Pb Adsorption in Histosols

ABSTRACT

Histosols have a high organic matter content and therefore a high variability of structures and chemical functional groups with adsorptive capacity. This study aimed to select the most appropriate models to describe the sorption phenomena of Cu and Pb in Histosols, identify the types of bonds between these metals and soil samples, and assess the influence of soil attributes and soil humic substance structures on these bonds. The Freundlich and Langmuir models were selected based on the values of the corrected Akaike information criterion and variation of Akaike information criterion as the best models for describing Cu and Pb sorption in Histosols. The values of the adsorption coefficients provided by the models indicated that Pb has higher affinity with the studied soil relative to Cu. However, Cu adsorption to soil occurs specifically and Pb is adsorbed nonspecifically. In general, the contents of N and fulvic acids were the factors that most influenced Pb sorption. Pb has a higher association with more aliphatic fulvic character structures, while Cu has a higher association with soil humic character structures. Therefore, compared to Cu, Pb in the studied Histosol has greater bioavailability potential and, consequently, greater risks of contamination and entering the food chain.     

不同腐解期玉米秸秆对塿土胡敏酸基本性质及级分变异的影响

采用田间腐解试验,在研究不同腐解期玉米秸秆对土壤胡敏酸性质影响的基础上,利用酒精分级沉淀法对土壤胡敏酸进行分级,研究了不同腐解期土壤胡敏酸级分组成及性质变化.结果表明,在整个腐解过程中土壤胡敏酸由A型转化为P型又转化为A型,呈现由复杂到简单又到复杂的变化趋势.不同腐解期土壤胡敏酸的级分组成不同.玉米秸秆更新土壤胡敏酸过程是一个双向过程,一方面使胡敏酸中结构复杂成分(级分1、2、3)向简单化发展,另一方面一些小分子胡敏酸(级分6、7)随时间推移按Rp→P→A途径逐渐缩合.     

Combined quantum and molecular mechanics calculations on metalloproteins

The combination of quantum mechanics and molecular mechanics (QM/MM) methods is one of the most promising approaches to study the structure, function and properties of proteins. The number of QM/MM applications on metalloproteins is steadily increasing, especially studies with density functional methods on redox-active metal centres. Recent developments include new parameterised methods to treat covalent bonds between the quantum and classical systems, methods to obtain free energy from QM/MM results, and the combination of quantum chemistry and protein crystallography.     

Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution

We compare the conformational distributions of Ace-Ala-Nme and Ace-Gly-Nme sampled in long simulations with several molecular mechanics (MM) force fields and with a fast combined quantum mechanics/molecular mechanics (QM/MM) force field, in which the solute's intramolecular energy and forces are calculated with the self-consistent charge density functional tight binding method (SCCDFTB), and the solvent is represented by either one of the well-known SPC and TIP3P models. All MM force fields give two main states for Ace-Ala-Nme, beta and alpha separated by free energy barriers, but the ratio in which these are sampled varies by a factor of 30, from a high in favor of beta of 6 to a low of 1/5. The frequency of transitions between states is particularly low with the amber and charmm force fields, for which the distributions are noticeably narrower, and the energy barriers between states higher. The lower of the two barriers lies between alpha and beta at values of psi near 0 for all MM simulations except for charmm22. The results of the QM/MM simulations vary less with the choice of MM force field; the ratio beta/alpha varies between 1.5 and 2.2, the easy pass lies at psi near 0, and transitions between states are more frequent than for amber and charmm, but less frequent than for cedar. For Ace-Gly-Nme, all force fields locate a diffuse stable region around phi = pi and psi = pi, whereas the amber force field gives two additional densely sampled states near phi = +/-100 degrees and psi = 0, which are also found with the QM/MM force field. For both solutes, the distribution from the QM/MM simulation shows greater similarity with the distribution in high-resolution protein structures than is the case for any of the MM simulations.     

Turnover of14C-labelled oat residues and small molecular organic compounds in two soils under different levels of mineral nutrition

Mineralization and redistribution of carbon from¹⁴C-labelled oat shoots and [¹⁴C(U)] labelled glucose, leucine, acetate and phenylacetate were studied in light loamy sand and medium clay loam under different levels of mineral nutrition. Losses of mineralized¹⁴C as CO₂ were greater in the sandy soil than in the clay soil. NPK and NPK+Ca fertilization increased the rates of decay of the introduced plant organic matter. Among the small molecular organic compounds glucose was degraded fastest and phenylacetate slowest. Incorporation of radioactive carbon into humus fractions varied and depended on the nature of the compound introduced and on the soil type. Carbon of glucose, phenylacetate and acetate was mainly incorporated into fulvic acids, whereas¹⁴C of leucine was almost evenly distributed between humic and fulvic acids and¹⁴C of oat residues in fulvic acids and humin fractions. There was significantly higher incorporation of¹⁴C into humic acids and lower incorporation into humins in the sandy soil compared to the clay soil. NPK+Ca decreased the conversion of¹⁴C from phenylacetate and acetate to bitumens and increased its content in humic acids, particularly in the clay soil. The incorporation of¹⁴C from phenylacetate to humins benefitted from mineral fertilization during the first 30 days of the experiment in both soils.     

The role of hydrophobic properties of chemicals in promoting allosteric reactions

An allosteric reaction has been found in a variety of instances where an inverted parabolic relationship between biological activity and hydrophobicity is apparent, that is the activity first decreases as hydrophobicity increases and after a certain point, activity begins to increase. This could be attributed to the ligands causing a change in the receptor structure. In this report, the role of hydrophobic properties of chemicals in promoting allosteric reactions have been discussed in term of hydrophobicity (logP) by the formulation of a total number of 50 QSAR equations. The QSAR model of this type may be represented by Eq. I.     

有机物质对土壤镉有效性的影响研究综述

土壤中的低分子有机酸和腐殖酸对镉的有效性有重要作用。根系分泌的低分子量有机酸能提高土壤镉的可提取率、移动性和生物有效性,但是更大分子量的有机酸EDTA却抑制植物对镉的吸收,腐殖酸促进土壤镉的溶解性;因腐殖酸组分和环境条件,腐殖酸能够促进也能抑制土壤镉活性,因此有必要深入研究影响腐殖酸固定镉的因素,以达到利用有机质抑制土壤镉活性的目的。     

Energy-minimized structures and packing states of a homologous series of mixed-chain phosphatidylcholines: a molecular mechanics study on the diglyceride moieties.

Phosphatidylcholines or C(X):C(Y)PC, quantitatively the most abundant lipids in animal cell membranes, are structurally composed of two parts: a headgroup and a diglyceride. The diglyceride moiety consists of the glycerol backbone and two acyl chains. It is the wide diversity of the acyl chains, or the large variations in X and Y in C(X):C(Y)PC, that makes the family of phosphatidylcholines an extremely complex mixture of different molecular species. Since most of the physical properties of phospholipids with the same headgroup depend strongly on the structures of the lipid acyl chains, the energy-minimized structure and steric energy of each diglyceride moiety of a series of 14 molecular species of phosphatidylcholines with molecular weights identical to that of dimyristoylphosphatidylcholine without the headgroup are determined in this communication by molecular mechanics (MM) calculations. Results of two types of trans-bilayer dimer for each of the 14 molecular species of phosphatidylcholines are also presented; specifically, the dimeric structures are constructed initially based on the partially interdigitated and mixed interdigitated packing motifs followed subsequently by the energy-minimized refinement with MM calculations. Finally, tetramers with various structures to model the lateral lipid-lipid interactions in a lipid bilayer are considered. Results of laborious MM calculations show that saturated diacyl C(X):C(Y)PC with delta C/CL values greater than 0.41 prefer topologically to assemble into tetramers of the mixed interdigitated motif, and those with delta C/CL values less than 0.41 prefer to assemble into tetramers with a repertoire of the partially interdigitated motif. Here, delta C/CL, a lipid asymmetry parameter, is defined as the normalized acyl chain length difference between the sn-1 and sn-2 acyl chains for a C(X):C(Y)PC molecule; an increase in delta C/CL value is an indication of increasing asymmetry between the two lipid acyl chains. These computational results are in complete accord with the calorimetric data presented previously from this laboratory (H-n. Lin, Z-q. Wang, and C. Huang. 1991. Biochim. Biophys. Acta. 1067:17-28).     

A QM/MM analysis of the conformations of crystalline sucrose moieties

Both ab initio quantum mechanics (QM) and molecular mechanics (MM) were used to produce a hybrid energy surface for sucrose that simultaneously provides low energies for conformations that are observed in crystal structures and high energies for most unobserved structures. HF/6-31G* QM energies were calculated for an analogue based on tetrahydropyran (THP) and tetrahydrofuran (THF). Remaining contributions to the potential energy of sucrose were calculated with MM. To do this, the MM surface for the analogue was subtracted from the MM surface for the disaccharide, and the QM surface for the analogue was added. Prediction of the distribution of observable geometries was enhanced by reducing the strength of the hydrogen bonding. Reduced hydrogen-bonding strength is probably useful because many crystalline sucrose moieties do not have intramolecular hydrogen bonds between the fructose and glucose residues. Therefore, hydrogen bonding does not play a large role in determining the molecular conformation. On the hybrid energy surface that was constructed with a dielectric constant of 3.5, the average potential energy of 23 sucrose moieties from crystal structures is 1.16 kcal/mol, and the population of observed structures drops off exponentially as the energy increases.     

Quantitative analysis of the relationship between structure and antioxidant activity of tripeptides

Peptides from enzymatic hydrolysates of food proteins exhibit significant antioxidant activity. Several studies have attempted to determine the factors contributing to the antioxidant activity of peptides; however, the physicochemical properties and factors essential for the antioxidant activity of peptides are still unclear. In this study, in order to clarify the factors important for peptide antioxidant activity based on the properties of component amino acids, 55 tripeptides were synthesized from 20 natural amino acids and their antioxidant activity was measured using the Trolox equivalent antioxidant capacity (TEAC) assay system. The tripeptides were divided into two data sets: a training set comprising 50 compounds and a validated set comprising five compounds. The structure‐activity relationship of the training set was then analyzed using classical quantitative structure‐activity relationship (QSAR) analysis. The study findings demonstrate that the presence of a cysteine residue at any position, an aromatic amino acid at the C‐terminus, higher hydrophobicity of the N‐terminal residue, and smaller HOMO‐LUMO energy gap of the middle residue can significantly enhance the antioxidant activity. The activities of the five validated compounds were predicted using the constructed QSAR model, and a good correlation between measured and predicted activities was observed. The information obtained from the QSAR model could be useful for effective production of antioxidant peptides from food proteins such as egg white proteins.     

Effects of different organic waste amendments on soil microaggregates stability and molecular sizes of humic substances

Three soils which had been amended for several years with pig slurry, cattle slurry, and sewage sludge were dry-sieved to obtain microaggregates in the size range of 250–125, 125–50, and <50 μm. With amendments, aggregate size distribution of whole soils was shifted to larger sizes, especially for the most fragile soil, whereas percent content of microaggregates decreased except for the lower size aggregates of the fragile soil. Particle size distribution of microaggregates revealed an increase in percent sand and a reduction of percent silt and clay in the <50 μg size fraction for all soils. These results showed the aggregation effect induced by the organic waste additions. Aggregate stability of microaggregates revealed significant correlation with humic substances content (humic acids alone and humic plus fulvic acids) and non significant with total organic matter substantiating the belief that humic substances are the predominant binding agents in this aggregation range. Molecular weight distribution of humic acids extracted from microaggregates of unamended soils demonstrated that the lower the soil aggregate size distribution, the larger the contribution of the high molecular weight fraction. All microaggregates from amended soils showed a progressive increase of the high molecular weight humic acids with decreasing size, reaching a maximum in the <50 μm fraction. In this aggregate size a parallel enhancement of the aggregate stability was also evident. It is concluded that a close relationship exists between aggregate stability and high molecular weight humic substances. Additions to soils of organic material containing high molecular weight constituents would represent a useful management practice to improve aggregate stability.     

Changes in the Structure and Properties of Alkali-Soluble Humic Substances in Phosphorus-Enriched Gray Forest Soil

The dynamics of spectral and kinetic properties of alkali-soluble humic substances in the gray forest soil were studied in the course of its incubation with NH₄H₂PO₄ (44.5 mg P per 100 g soil) for seven days, one year, and three years. The results provided evidence for consistent changes in the energy state of electrons in the functional groups of humic molecules extracted from the phosphorus-enriched soil. The structure of these molecules markedly changed by the end of the experiment, which was manifested in the increased number of coupled chromophores (due to the formation of additional C=C bonds) and the accumulation of new strongly polar functional groups (P=O). These changes provided for an increased solubility of soil humus in 0.1 N NaOH, higher saturation of dissolved humic substances with metals, and a different pattern of the distribution of carbon, metals, and phosphorus between the fractions of humic and fulvic acids.     

Isolation of soil Streptomyces strains capable of degrading humic acids and analysis of their peroxidase activity

Abstract Fifteen Streptomyces strains capable of decolorizing humic acids in presence of glucose were isolated from soil samples using the dilute suspension technique and spread on agar plates. Six strains, displaying a significant and stable activity, were selected for further characterization. Some features of these isolates (carbon source utilization, enzyme production, antibiotic resistance) were compared with those of the reference strain Streptomyces viridosporus ATCC 39115. Degradation properties studied in batch cultures at pH 7.0 showed that the catabolic activity on humic acids was generally stimulated by incubation with 100% oxygen and was cell surface-associated. Peroxidase activity from cell-free extracts was analysed by using the oxidation of N,N,N′,N′-tetramethyl-phenylene-diamine. PAGE analysis revealed the existence of two major types of peroxidases (molecular mass: about 39.2 and 61.6 kDa), dividing the strains into two groups. The role of cell surface-associated peroxidase activity in the breakdown of humic acids is discussed.