Mathematical simulation of complex formation of protein molecules allowing for their domain structure

A physical model of the interactions between protein molecules has been presented and an analysis of their propensity to form complex biological complexes has been performed. The reactivities of proteins have been studied using electrostatics methods based on the example of the histone chaperone Nap1 and histones H2A and H2B. The capability of proteins to form stable biological complexes that allow for different segments of amino acid sequences has been analyzed. The ability of protein molecules to form compounds has been considered by calculating matrices of electrostatic potential energy of amino acid residues constituting the polypeptide chain. The method of block matrices has been used in the analysis of the ability of protein molecules to form complex biological compounds.     

Theoretical study of the HXYH dimers (X,Y = O,S, Se). Hydrogen bonding and chalcogen–chalcogen interactions

A theoretical study of the HXYH (X, Y?=?O, S and Se) monomers and dimers has been carried out by means of MP2 computational methods. For the monomers, isomerization (H₂X=Y//HXYH) and rotational transition state barriers have been calculated. Additionally, the molecular electrostatic potential of the isolated monomers has also been analysed. Due to the chiral nature of these compounds, homo and heterochiral dimers have been explored. The number of minima found for the dimers range between 13 and 22. The electron density of the complexes has been characterized with the Atoms in Molecules (AIM) methodology finding a large variety of interactions. The DFT-SAPT method has been used to analyse the components of the interaction energies. Concerning chalcogen–chalcogen interactions, although the most stable minima are formed through hydrogen bonds (especially if OH groups are present in the molecules) as the size of the atoms involved in the interaction increase, the chalcogen–chalcogen contacts become more important.     

Mathematical modeling of the temperature effect on the character of linking between monomeric proteins in aqueous solutions

Technical Physics - This work is devoted to the mathematical modeling of the temperature effect on the stability of H2A–H2B and Н3–H4 histone dimers by studying their behavior in...     

Mathematical modeling the formation of a histone octamer

A physical model of the interaction of protein molecules and their ability to form complex biological systems for the in vitro case in a solution of monovalent salt has been developed. Their reactive abilities using the methods of electrostatics based on the example of the step-by-step formation of the histone octamer from the H2A, H2B, H3, and H4 proteins have been studied. To analyze the ability of protein molecules to form compounds the matrix of potential energy of interactions between protein molecules in solutions with different concentrations of monovalent salt has been examined.     

硼、氮取代二聚苯中碳原子导致层间相互作用本质变化研究

在MP2/aug-cc-pVTZ水平下优化了二聚苯及其碳被硼、氮原子取代的几何构型;计算了这些二聚体的CCSD(T)/CBS相互作用能;并用SAPT2+/aug-cc-pVDZ分析了相互作用能成分.探索了硼、氮取代二聚苯中碳原子所导致层间相互作用本质变化.结果表明:稳定构型而言,从苯(C_6H_6)、1-氮-2-硼杂苯(BNC_4H_6)、1,3-二氮-2,4-二硼杂苯(B_2N_2C_2H_6)二聚体的平行移位(PD)构型向无机苯(B_3N_3H_6)二聚体的夹心(S)构型转变,其中C_6H_6和B_3N_3H_6二聚体稳定构型的堆叠型式分别与之相对应的石墨烯(GE)和六方氮化硼(h-BN)2D层间材料的堆叠型式相一致.硼、氮原子取代二聚苯中的碳原子后使其相互作用能增大,其中BNC_4H_6和B_2N_2C_2H_6二聚体的相互作用能增大较为明显.所研究体系二聚体稳定构型均以色散能为主导、静电能次之、诱导能相对较小.硼、氮取代二聚苯中碳原子后其静电能对总吸引能的贡献明显增大.     

Interaction of low-energy Cu2 dimers with copper clusters on the graphite surface

The sputtering of clusters consisting of 13, 27, and 75 copper atoms from the (0001) graphite surface under bombardment by Cu₂ dimers with energies of 100, 200, and 400 eV has been simulated using the molecular dynamics method. A comparative analysis of the distributions of backscattered particles and their energies over polar angles and the energy distributions of sputtered atoms has been performed. The factors responsible for the large sputtering yield from surface clusters under their bombardment with dimers as compared to copper and xenon monomers have been discussed. It has been demonstrated that, in the case of bombardment with dimers, the substantial role in the sputtering of surface clusters is played by the overlap of collision cascades initiated by each atom of the incident dimer. The differences in the sputtering under cluster and atom bombardments are especially pronounced in the case of large surface clusters.     

KDP晶格振动模和生长机制的拉曼光谱研究(英文)

用空间群理论分析和指认了KDP晶体的拉曼活性晶格振动模 ,测量了晶体以及生长溶液的拉曼光谱 ,重点分析了出现在固 /液界面附近的 91 6cm- 1拉曼峰 ,该峰被指认为扭曲的P(OH) 2 集团反对称伸缩振动。依据本文的理论分析和实验测量 ,我们认为H2 PO- 4阴离子集团的二聚物可能是KDP晶体的生长基元。     

Solid-state photodimerization of 4-aryl-1,4-dihydropyridines studied by C CPMAS NMR spectroscopy

¹³C CPMAS NMR spectroscopy has been applied to monitor the solid-state reaction of two different photodimerizing 4-phenyl-1,4-dihydropyridines yielding a cage dimer in one case and an anti-dimer in the other case. The spectra of the reacting monomers exhibit a magnetical inequivalence of chemically equivalent CO and C2/4 carbon atoms caused by a rotation of the pseudoaxially oriented 4-phenyl substituent out off the plane through N1, C3, C8 which could be determined by X-ray crystal structure analyses of the centrosymmetrically arranged monomers. The ¹³C CPMAS NMR monitoring of the cage dimer formation proves that the reaction takes place in two steps via a syn-dimer for which a non-symmetrical structure was derived from the spectrum. The non-symmetrical structure was confirmed by X-ray crystal structure analysis of one structurally related derivative. A centrosymmetric structure for both the finally formed cage dimer and the anti-dimer of the other monitored photoreaction was proved by their spectra with one set of signals for each half of the dimers, respectively. Thus, conformational properties of the molecules as well as the symmetry of the products can be directly derived from the ¹³C CPMAS NMR spectra.     

How does the ferritin core form?

Ferritin stores iron as ferrihydrite inside a shell composed of H and L protein chains. H chains contain ferroxidase centres catalysing Fe²⁺ oxidation, while L chains lack these centres but seem to promote ferrihydrite nucleation. Mössbauer spectroscopic studies of recombinant H-chain ferritins show the following: (1) fast Fe²⁺ oxidation is associated with the formation of Fe³⁺ dimers at the ferroxidase centre; (2) within 30 min, a portion of the dimers have split to Fe³⁺ monomers and some monomers have moved to the threefold channels; (3) over longer times, a trend dimer monomer core is established. Core formation is accelerated if L chains are present.     

Cu2+ Coordination of Covalently Cross-linked β-Amyloid Dimers

Alzheimer’s disease (AD) is a neurodegenerative disorder characterized by deposition of extracellular amyloid plaques comprised from fibrillar aggregates of the amyloid-β peptide (Aβ). Cu²⁺ interactions with Aβ appear to be involved in both the production of reactive oxygen species and the misfolding of Aβ into oligomeric intermediates including covalently cross-linked dimers. We have previously investigated the Cu²⁺ coordination of Aβ monomers in detail, whilst others have shown that Aβ fibrils coordinate Cu²⁺ in a similar manner to Aβ monomers. However, the coordination of low-molecular-weight Aβ species, which are believed to be responsible for neuronal dysfunction in AD, has not been widely investigated. Here, we report the first study of Cu²⁺ coordination by synthetic Aβ dimers containing an artificial diaminopimelic acid (DAP) or a dityrosine cross-link at residue 10. Our preliminary findings show that dityrosine cross-linking imparts unique structural constraints, resulting in Cu²⁺ coordination distinct from Aβ monomers and fibrils, which may be relevant to the greater toxicity of low-molecular-weight Aβ oligomers in AD.     

Synthesis and luminescence properties of dye-doped deoxyribonucleic acid films

Dye-doped deoxyribonucleic acids (DNA)–tetradecyltrimethylammonium (TTA) films have been prepared. Rhodamine 6G, known as laser dyes, can be spontaneously doped by immersing the DNA–TTA film in rhodamine 6G-acetonitrile solutions. It is surmised that rhodamine 6G monomers and dimers diffuse within the hydrophobic TTA sites, and then monomers presumably intercalate between adjacent base pairs of DNA. Optical absorption spectra reveal that rhodamine 6G molecules in the sample undergo an unusual transformation from the dimer state to the monomer state with the elapse of time. Rhidamine 6G molecules doped in DNA–TTA show enhanced photostability and concentration quenching than those in PMMA. The environment, conformation and chemical stability of rhodamine 6G are different between DNA–TTA and PMMA, and are presumably modified by the intercalation.     

Investigation of the IR spectra of weakly hydrogen-bonded complex Cl<Subscript>3</Subscript>CH…O(CD<Subscript>3</Subscript>)<Subscript>2</Subscript> in a cryosolution in liquid krypton

The IR absorption spectra of cryosolutions of chloroform, dimethyl ether, and their mixtures in liquefied krypton have been measured. It has been shown that, in solutions of mixtures, Cl₃CH…O(CD₃)₂ complexes with a weak hydrogen bond are formed. The spectral characteristics of individual absorption bands that refer to proton donors and to proton acceptors have been determined. From temperature measurements of the integrated intensities of the bands of monomers and of the complex (T ~ 120–160 K), the enthalpy of the complex formation has been estimated. The measurement data have been analyzed in comparison with the results of ab initio calculations in terms of the МР2/6-311++G(2df, 2pd) approximation. The analysis has been done taking into account peculiarities of the dipole moment function of chloroform and possible effects of the anharmonic interaction between the С–Н stretching vibration and the overtone of the Cl–C–H bending vibration.     

Quenching of fluorescence of porphyrin molecules in their association in binary solutions

It has been established that the absorption and fluorescence spectra of octaethylporphin (OEP), mesotetraphenylporphin (TPhP), and its complex with zinc (Zn-TPhP) in glycerol doped with dimethylformamide (DMF) or ethanol differ from the analogous spectra of these compounds in ethanol or DMF, which is due to the formation of associates of porphyrin molecules in solutions of OEP, TPhP, and An-TPhP with glycerol. For TPhP and Zn-TPhP, these differences are small, the maxima of the bands are shifted toward longer wavelengths by 3–5 nm, and their halfwidths are increased by ∼ 16%; for OEP these changes are more significant. It is shown that the duration of fluorescence of associates is much shorter than that of monomers. The probable mechanisms of quenching of the fluorescence of dimers (oligomers) of molecules were considered. It has been suggested that one of the reasons for the increased rates of deactivation of the excited states of dimers (oligomers) may be the decreased energy interval between the excited and ground states of associates as compared with that of monomers. Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 67, No. 1, pp. 21–25, January–February, 2000.     

Excited‐state hydrogen bonding dynamics of pyruvic acid and geminal‐diol, 2,2‐dihydroxypropanoic acid in aqueous solution: a DFT/TDDFT study

In this work, we present the optimized ground state geometrical structures, electronic excitation energies and corresponding oscillation strengths of the low‐lying electronically excited states for the isolated Tce‐CH3COCOOH and Tce‐CH3C(OH)2COOH as well as their corresponding hydrogen‐bonded dimers Tce‐CH3COCOOH‐H2O and Tce‐CH3C(OH)2COOH‐H2O through time‐dependent density functional theory method. It is found that the intermolecular hydrogen bonds C=O···H‐O are strengthened in the electronically excited states of the hydrogen‐bonded dimers Tce‐CH3COCOOH‐H2O and Tce‐CH3C(OH)2COOH‐H2O, in that the excitation energies of the related excited states for the hydrogen‐bonded dimers are decreased compared with those of the corresponding monomers. The calculated results are consistent with the rules that are first demonstrated by Zhao on the excited‐state hydrogen bonding dynamics. Copyright © 2012 John Wiley & Sons, Ltd.     

Infrared studies of matrix isolated sodium and potassium chloride and cyanide dimers

The infrared spectra of matrix isolated sodium and potassium chlorides and cyanides in different inert gas matrices were examined over the range 4000 cm^?1 to 33 cm^?1. A study of the effect of superheating the vapor species on the spectra has been carried out. Temperature cycling experiments have been pursued in an attempt to differentiate between bands due to monomers, dimers, and higher polymers. Isotopic frequency shifts were measured for a carbon-13 enriched sample of sodium cyanide and carbon-13 and nitrogen-15 enriched samples of potassium cyanide in the CN region. Symmetry force constants were calculated assuming a cyclic rhombic structure for the dimers. In the case of the cyanide dimer, the CN group of the molecule was considered as a halide atom. Finally a comparison is given between the symmetry force constants of the dimers of the alkali metal fluorides, cyanides and chlorides.     

Dimers and trimers of polycyclic aromatic hydrocarbons as models of graphene bilayers and trilayers: enhanced electron density at the edges

Structures of dimers and trimers of polycyclic aromatic hydrocarbons (PAHs) having zig-zag edges, and continuous electron density and molecular electrostatic potential (MEP) distributions in these systems were studied in gas phase. Dimers of benzene and naphthalene for which high-accuracy results are available were used to test the reliability of four different functionals of density functional theory in combination with the 6-31G(d,p) basis set. The dispersion-corrected WB97XD functional was found to be distinctly superior to the other three functionals used and was employed to study PAH dimers and trimers. Electronic structures and geometries of dimers of a four benzene ring and a nine benzene ring systems and trimers of the four benzene ring system were investigated. The dimers and trimers of PAHs were found to be of parallel-displaced type, as observed experimentally for graphene. The enhanced electron density edge effect found in the PAH monomers earlier is found to exist in the dimers and trimers also.     

HPLC-coupled spectroscopic techniques (UV, MS, NMR) for the structure elucidation of phthalides in Ligusticum chuanxiong

Ligusticum chuanxiong Hort., a plant that is frequently used in traditional Chinese medicine, has been studied using HPLC-coupled spectroscopic techniques such as HPLC-UV, HPLC-MS as well as HPLC-NMR. With the aid of these modern spectroscopic techniques, the main constituents, namely senkyunolide A, butylphthalide, neocnidilide and Z-ligustilide, have been characterized and identified. Phthalide dimers, present in smaller amounts, have been identified by HPLC-UV and HPLC-MS analysis and compared with reference compounds. Stereochemical features of some phthalide monomers have been determined by detailed spectroscopic studies for the first time.     

Orientational Ordering of the Near-Surface Layers of Nitrobenzene

Two types of absorption centers, one being related to monomers and the other to dimers, have been revealed by the method of statistical analysis of the normalized absorption spectra of a superthin interlayer of nitrobenzene of variable thickness formed on activated surfaces of quartz and barium fluoride and measured for different thicknesses of the interlayer. On a decrease in the interlayer thickness the concentration of dimers increases.     

Interaction studies of cysteine with Li+, Na+, K+, Be2+, Mg2+, and Ca2+ metal cation complexes

The coordination geometries, electronic features, metal ion affinities, entropies, and the energetics of Li⁺, Na⁺, K⁺, Be²⁺, Mg²⁺, and Ca²⁺ metal cations with different possible conformations of cysteine complexes were studied. The complexes were optimized using density functional theory (B3LYP) and second order Moller–Plesset Perturbation (MP2) theory methods using 6‐311 + +G** basis set. The interactions of the metal cations at different nucleophilic sites of cysteine conformations were considered after a careful selection among several binding sites. All the metal cations coordinate with cysteine in a tridentate manner and also the most preferred position for the interaction. It is found that, the overall structural parameters of cysteine are not altered by metal ion substitution, but, the metal ion‐binding site has undergone a noticeable change. All the complexes were characterized by an electrostatic interaction between ligand and metal ions that appears slightly more pronounced for lithium and beryllium metal complexes. The metal ion affinity (MIA) and basis set superposition error (BSSE) corrected interaction energy were also computed for all the complexes. The effect of metal cations on the infrared (IR) stretching vibrational modes of amino N? H bond, side chain thiol group S? H bond, hydroxyl O? H bond, and Carbonyl C?O bond in cysteine molecules have also been studied. The nature of the metal ion‐ligand bond and the coordination properties were examined using natural bond order (NBO) at bond critical point (electron density and their Laplacian of electron density) through Atoms in Molecules (AIM) analyses. Copyright © 2010 John Wiley & Sons, Ltd.     

EXAFS study of iron monomers and dimers isolated in solid argon

We report a study of local structure of iron monomers and dimers isolated in a rare gas Ar matrix using extended X-ray absorption fine structure measurements. The results have been compared with Mössbauer measurements on such systems. The interatomic distance found for Fe₂ in these measurements is 1.87 ± 0.13 Å.