Biomedical subjects

A V Nemukhin

Publications and source records attributed to A V Nemukhin.

5 recordsLinked to original sources

PubMed2005

Quantum chemical modeling of the reduction of cis-diammineplatinum(IV) tetrachloride [Pt(NH3)2Cl4] by methyl thiolate anion.

We present here both an ab initio and quantum mechanical/molecular mechanical (QM/MM) study of the cis-[Pt(NH3)2Cl4] complex reduction by methyl thiolate anion, SCH(-3), which is used as a model of glutathione. Geometry and electronic structure of cis-[Pt(NH3)2Cl4] are determined without and in aqueous medium. The mechanism of the reaction of reduction is characterized. The calculated activation energy of the reaction compares remarkably well with the experimental value.

Antineoplastic Agents↗

PubMed2004

Hybrid diatomics-in-molecules-based quantum mechanical/molecular mechanical approach applied to the modeling of structures and spectra of mixed molecular clusters Arn(HCl)m and Arn(HF)m.

A new hybrid QM/DIM approach aimed at describing equilibrium structures and spectroscopic properties of medium size mixed molecular clusters is developed. This methodology is applied to vibrational spectra of hydrogen chloride and hydrogen fluoride clusters with up to four monomer molecules embedded in argon shells Arn(H(Cl/F))m (n = 1-62, m = 1-4). The hydrogen halide complexes (QM part) are treated at the MP2/aug-cc-pVTZ level, while the interaction between HX molecules and Ar atoms (MM part) is described in terms of the semiempirical DIM methodology, based on the proper mixing between neutral and ionic states of the system [Grigorenko et al., J. Chem. Phys. 104, 5510 (1996)]. A detailed analysis of the resulting topology of the QM/DIM potential energy (hyper-)surface in the triatomic subsystem Ar-HX reveals more pronounced nonadditive atomic induction and dispersion contributions to the total interaction energy in the case of the Ar-HCl system. An extension of the original analytical DIM-based potential in the frame of the present model as well as the current limitations of the method are discussed. A modified algorithm for the gradient geometry optimization, along with partly analytical force constant matrix evaluation, is developed to treat large cages of argon atoms around molecular clusters. Calculated frequency redshifts of HX stretching vibrations in the mixed clusters relative to the isolated hydrogen-bonded complexes are in good agreement with experimental findings.

Journal Article↗

PubMed2003

Flexible effective fragment QM/MM method: validation through the challenging tests.

A new version of the QM/MM method, which is based on the effective fragment potential (EFP) methodology [Gordon, M. et al., J Phys Chem A 2001, 105, 293] but allows flexible fragments, is verified through calculations of model molecular systems suggested by different authors as challenging tests for QM/MM approaches. For each example, the results of QM/MM calculations for a partitioned system are compared to the results of an all-electron ab initio quantum chemical study of the entire system. In each case we were able to achieve approximately similar or better accuracy of the QM/MM results compared to those described in original publications. In all calculations we kept the same set of parameters of our QM/MM scheme. A new test example is considered when calculating the potential of internal rotation in the histidine dipeptide around the C(alpha)bond;C(beta) side chain bond.

Journal Article↗

PubMed2001

Formation of mixed d- and f-block metal clusters in inert matrices: comparison of the observed and theoretical optical spectra of AgHo.

The UV visible spectra obtained after simultaneous cocondensation of silver and holmium atoms with argon matrices at 9 K have been studied in the 200-800 nm region. While no new feature can be observed upon deposition, selective irradiation into both silver or holmium atomic absorptions results in growth of a new band at 430 nm, associated with formation of a mixed silver holmium species, tentatively assigned as AgHo. To support the assignment of the observed bands ab initio quantum chemical calculations were carried out for the dinuclear and trinuclear silver and holmium species, using pseudopotential approaches. Results for the electronic excitation energies and corresponding transition dipole moments for the diatomic molecules Ag2, Ho2, AgHo provide evidence that the 430 nm band should be attributed to the mixed cluster AgHo (theoretical band position at 436 nm), while the doublets at 498/504 and 558/563 nm belong to the homonuclear species Ho2 (theoretical values are at 482 and 562 nm). First conclusions are drawn with respect to the formation of the metal trimers Ho3, Ag2Ho, AgHo2.

Argon↗

PubMed2000

Spectroscopic study of low temperature interactions in metal-organic co-condensates.

The results on spectroscopic study of low temperature interactions of metal atoms, small clusters and nanoparticles with different organic and inorganic substances in the temperature range 12-300 K are presented. Complexation and reactions of atoms and clusters of magnesium, samarium and silver with carbon dioxide, ethylene and some mesogenic cyanophenyls were studied by the technique of matrix isolation and low temperature co-condensation of metal and ligand vapors, low temperature UV-Vis, IR- and ESR-spectroscopy in combination with quantum chemistry calculations. It was shown that cryochemical reactions of metal particles of different sizes reflected the system's redundant energy.

Carbon Dioxide↗