Interaction of hydrogen peroxide molecules with non-specific DNA recognition sites

Ion beam therapy is one of the most progressive methods in cancer treatment. Studies of the water radiolysis process show that the most long-living species that occur in the medium of a biological cell under the action of ionizing irradiation are hydrogen peroxide (H$_2$O$_2$) molecules. But the role of H$_2$O$_2$ molecules in the DNA deactivation of cancer cells in ion beam therapy has not been determined yet. In the present paper, the competitive interaction of hydrogen peroxide and water molecules with atomic groups of non-specific DNA recognition sites (phosphate groups PO$_4$) is investigated. The interaction energies and optimized spatial configurations of the considered molecular complexes are calculated with the help of molecular mechanics method and quantum chemistry approach. The results show that the H$_2$O$_2$ molecule can form a complex with the PO$_4$ group (with and without a sodium counterion) that is more energetically stable than the same complex with the water molecule. Formation of such complexes can block genetic information transfer processes in cancer cells and can be an important factor during ion beam therapy treatment

Complexes of hydrogen peroxide and DNA phosphate group in quantum chemical calculations

Background: Molecules of hydrogen peroxide (H2O2) can be formed during radiolysis process in water medium after irradiation. A hypothesis about the possible role of hydrogen peroxide in blocking of processes of nonspecific DNA recognition by proteins is proposed in [1]. As one of the most long-living products, H2O2 molecules can diffuse considerable distances in the intracellular medium and reach DNA in the cell nucleus and form complexes with macromolecule phosphate groups. To confirm this hypothesis, the quantum chemical calculations of complexes structure of hydrogen peroxide molecule with atomic groups of the DNA backbone are performed. Objectives: To determine the optimal geometries and formation energies of stable complexes of hydrogen peroxide with DNA phosphate group. To perform a comparative analysis of hydrogen peroxide and water molecules binding to phosphate group based on quantum chemical calculations. Materials and Methods: The complexes which consist of phosphate group, hydrogen peroxide, water molecules, and sodium counterion are analyzed. The optimization of complex geometry and energy calculations is performed using the methods of quantum chemistry within Gaussian 03 software: HF/6-31+G(d,p), MP2/6-31+G(d,p), B3LYP/6-31+G(d,p). Results: This research shows that the hydrogen peroxide molecule as well as water molecule can form stable complexes with phosphate group, especially with the presence of sodium counterion Na+. The results of complex formation calculations with atom-atom potential functions method are confirmed. It is shown that the presence of sodium counterion significantly influences the geometry of the hydrogen peroxide complex with the phosphate group. The performed calculations indicate the possibility of hydrogen peroxide geometry change in the processes of complex formation. Conclusions: The obtained results confirm the possibility of stable complexes forming for hydrogen peroxide and phosphate group. Prolonged situation of H2O2 molecule near the DNA backbone may block the nucleic-protein recognition processes as well as damage the macromolecule via decay into OH-radicals in close proximity to double helix

Theoretical investigation on H2O2-Ng (He, Ne, Ar, Kr, Xe, and Rn) complexes suitable for stereodynamics : interactions and thermal chiral rate consequences

Although molecular collisions of noble gases (Ng) can be theoretically used to distinguish between the enantiomers of hydrogen peroxide - H2O2 (HP), little is known about the effects of HP-Ng interactions on the chiral rate. In this work, the chiral rate as a function of temperature (CRT) between enantiomeric conformations of HP and Ng (Ng=He, Ne, Ar, Kr, Xe, and Rn) are presented at MP2(full)/aug-cc-pVTZ level of theory through a fully basis set superposition error (BSSE) corrected potential energy surface. The results show that: (a) the CRT is highly affected even at a small decrease in the height of trans-barrier; (b) its smallest values occur with Ne for all temperatures between 100 and 4,000 K; (c) that the decrease of CRT shows an inverse correlation with respect to the average valence electron energy of the Ng and (d) Ne and He may be the noble gases more suitable for study the oriented collision dynamics of HP. In addition to binding energies, the electron density ρ and its Laplacian ∇2ρ topological analyses were also performed within the atoms in molecules (AIM) theory in order to determine the nature of the HP-Ng interactions. The results of this work provide a more complete foundation on experiments to study HP's chirality using Ng in crossed molecular beams without a light source

Feature Papers in Compounds

This book represents a collection of contributions in the field of the synthesis and characterization of chemical compounds, natural products, chemical reactivity, and computational chemistry. Among its contents, the reader will find high-quality, peer-reviewed research and review articles that were published in the open access journal Compounds by members of the Editorial Board and the authors invited by the Editorial Office and Editor-in-Chief

Cornerstones in Contemporary Inorganic Chemistry

A collection of essential research articles and scientific reviews covering some of the most pertinent and topical areas of study that currently constitute Inorganic Chemistry in the early 21st century

A foundation model for atomistic materials chemistry

Machine-learned force fields have transformed the atomistic modelling of materials by enabling simulations of ab initio quality on unprecedented time and length scales. However, they are currently limited by: (i) the significant computational and human effort that must go into development and validation of potentials for each particular system of interest; and (ii) a general lack of transferability from one chemical system to the next. Here, using the state-of-the-art MACE architecture we introduce a single general-purpose ML model, trained on a public database of 150k inorganic crystals, that is capable of running stable molecular dynamics on molecules and materials. We demonstrate the power of the MACE-MP-0 model - and its qualitative and at times quantitative accuracy - on a diverse set problems in the physical sciences, including the properties of solids, liquids, gases, chemical reactions, interfaces and even the dynamics of a small protein. The model can be applied out of the box and as a starting or "foundation model" for any atomistic system of interest and is thus a step towards democratising the revolution of ML force fields by lowering the barriers to entry.Comment: 119 pages, 63 figures, 37MB PD

Investigação da força e natureza da ligação intermolecular fraca nos adutos formados por gases nobres e as moléculas H2S, CH3OH e H2O2

Tese (doutorado)—Universidade de Brasília, Instituto de Física, Programa de Pós-Graduação em Física, 2020.Neste trabalho, é realizado uma investigação detalhada da força e natureza das in- terações intermoleculares fracas responsáveis pela manutenção dos agregados formados pelos gases nobres Ng (Ng=He, Ne, Ar, Kr, Xe e Rn) e as moléculas de sulfeto de hi- drogênio (H2S), metanol (CH3OH) e peróxido de hidrogênio (H2O2). Para realizar este estudo, foram determinadas uma série de propriedades tais como a densidade eletrônica, deslocamento de carga, orbitais de fronteira HOMO e LUMO, análise do orbital de ligação natural, decomposição da energia de interação (termos eletrostático, indução, dispersão e troca ou Exchange) e do laplaciano da densidade de eletrônica. Todas estas propriedades foram calculadas considerando as conformações de mínimo absoluto dos agregados H2S- Ng e CH3OH-Ng e as estruturas enantioméricas dos complexos H2O2-Ng. Os resultados obtidos revelam que os adutos H2S-Ng se mantêm formados por interações do tipo van der Waals, ou seja, pelo equilíbrio favorável entre forças de dispersão de longo alcance, repulsão de Pauli de curto alcance e por deslocamentos de carga estabilizadores. Curvas de deslocamento de carga sugerem que os átomos de Ng (para todos os sistemas H2S-Ng) são fracamente polarizados e com a densidade de elétrons fluindo do átomo Ng para o en- xofre. Para os agregados formados pela molécula de metanol e os gases nobres verificou-se, através da análise de deslocamento de carga e a decomposição da interação intermolecular, que a estabilização da transferência de carga desempenha um papel menor e que os ter- mos de troca (repulsivo) e dispersão (atrativo) são os que mais contribuem para a energia de interação do complexo. Para as conformações enantioméricas dos complexos H2O2-Ng, os efeitos de polarização são mais apreciáveis nos agregados formados pelos átomos Xe e Rn e que um deslocamento líquido de carga ocorre do átomo de Ng para a molécula de peróxido de hidrogênio. Além disso, verificou-se que a maior transferência de carga ocorre para a configuração da barreira-cis, sugerindo que para esta estrutura o deslocamento de carga é intensificado pelas duas interações simétricas que os dois átomos de hidrogênio da molécula H2O2 fazem com o átomo Ng. Finalmente, observou-se que, para todas as conformações enantioméricas consideradas, o termo que mais contribui para a interação dos adutos H2O2-Ng foi o da dispersão, indicando que esses complexos são de fato do tipo van der Waals.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES).In this work, a detailed investigation of the strength and nature of the weak intermolecular interactions responsible for the maintenance of the aggregates formed by the noble gases Ng (Ng = He, Ne, Ar, Kr, Xe and Rn) and the hydrogen sulfide molecules (H2S), metha- nol (CH3OH) and hydrogen peroxide (H2O2). In order to carry out this study, a series of properties were determined such as electronic density, charge displacement, HOMO and LUMO boundary orbitals, analysis of the natural bonding orbital, decomposition of the interaction energy (electrostatic, induction, dispersion and exchange terms) and the Laplacian of electronic density. All of these properties were calculated considering the absolute minimum conformations of the H2S-Ng and CH3OH-Ng aggregates and the enantiomeric structures of the H2O2-Ng complexes. The obtained results reveal that the H2S-Ng adducts remain formed by van der Waals interactions, that is, by the favorable balance between long-range dispersion forces, short-range Pauli repulsion and by charge displacement stabilizers. Charge displacement curves suggest that the Ng atoms (for all H2S-Ng systems) are weakly polarized and with the electron density flowing from the Ng atom to the sulfur. For aggregates formed by the methanol and Ng it was found, through the analysis of charge displacement and the decomposition of intermolecular interaction, that the stabilization of charge transfer plays a minor role and that the terms of exchange (repulsive) and dispersion (attractive) are the ones that most contribute to the complex’s interaction energy. For the enantiomeric conformations of the H2O2-Ng complexes, the po- larization effects are more appreciable in the aggregates formed by the Xe and Rn atoms and that a net charge displacement occurs from the Ng atom to the peroxide of hydro- gen. In addition, it was found that the greatest charge transfer occurs for the cis-barrier configuration, suggesting that for this structure the charge displacement is enhanced by the two symmetrical interactions that the two hydrogen atoms of the H2O2 do with the Ng atom. Finally, it was observed that, for all considered enantiomeric conformations, the term that most contributes to the interaction of H2O2-Ng adducts was the dispersion, indicating that these complexes are in fact van Waals type

Efficient model chemistries for peptides. I. Split-valence Gaussian basis sets and the heterolevel approximation in RHF and MP2

We present an exhaustive study of more than 250 ab initio potential energy surfaces (PESs) of the model dipeptide HCO-L-Ala-NH2. The model chemistries (MCs) used are constructed as homo- and heterolevels involving possibly different RHF and MP2 calculations for the geometry and the energy. The basis sets used belong to a sample of 39 selected representants from Pople's split-valence families, ranging from the small 3-21G to the large 6-311++G(2df,2pd). The reference PES to which the rest are compared is the MP2/6-311++G(2df,2pd) homolevel, which, as far as we are aware, is the more accurate PES of a dipeptide in the literature. The aim of the study presented is twofold: On the one hand, the evaluation of the influence of polarization and diffuse functions in the basis set, distinguishing between those placed at 1st-row atoms and those placed at hydrogens, as well as the effect of different contraction and valence splitting schemes. On the other hand, the investigation of the heterolevel assumption, which is defined here to be that which states that heterolevel MCs are more efficient than homolevel MCs. The heterolevel approximation is very commonly used in the literature, but it is seldom checked. As far as we know, the only tests for peptides or related systems, have been performed using a small number of conformers, and this is the first time that this potentially very economical approximation is tested in full PESs. In order to achieve these goals, all data sets have been compared and analyzed in a way which captures the nearness concept in the space of MCs.Comment: 54 pages, 16 figures, LaTeX, AMSTeX, Submitted to J. Comp. Che

Theoretical Screening of 2D Materials as High-Efficiency Catalysts for Energy Conversion and Storage Applications

This Ph.D. thesis focuses on the exploration and design of new electrocatalysts; the theoretical screening and establishment of new high-efficiency catalysts for electrochemical reactions on 2D materials is based on extensive research, which provides a new route for designing heterogeneous catalysis and paves the way for the development of better electrochemical energy storage and conversion. Theoretical screening focuses on designing more selective, stable, and catalytically active electrocatalysts at a lower cost and finally replace commonplace catalysts. Achieving this requires sufficient theoretical knowledge of how a catalyst functions and works, including the active sites, reaction mechanisms, and expected products. The ultimate goal is to have a sufficient understanding of the significant influencing factors that determine the performance of a catalyst, which can be evaluated using the binding energy of the intermediates or D band center as descriptors. However, it is challenging to provide detailed information on reaction mechanisms using only experimental techniques. Extensive theoretical screening based on density functional theory (DFT) approaches has been employed to obtain basic guidelines for catalyst design. In this thesis, the electrocatalytic mechanisms of some representative electrochemical reactions are taken as examples to comprehensively analyze the present situation in terms of electrocatalyst technology that is to be used for application in energy storage and conversion devices, such as the oxygen reduction reaction (ORR) in fuel cells, carbon dioxide reduction (CO2 RR) in capturing CO2 , nitrogen reduction (NRR) in nitrogen fixation, and the nitric oxide (NO) reduction of ammonia (NORR) on two-dimensional (2D) materials. Theoretical screening is utilized to summarize the detailed design of the electrocatalyst. The understanding of 2D materials as catalysts for electrochemical catalysis can be broadened from various perspectives. The theoretical screening method guides the further development and discovery of highly efficient and inexpensive electrochemical catalysts, which can help confirm the preferable mechanism path to develop the control step of a reaction system. Achieving efficient catalytic activity for electrochemical reactions in promising future catalysts requires people to focus on highly flexible active sites, sufficient activity, selectivity, and a large species. Here, several great and novel 2D materials are considered as catalysts for electrochemical reduction, including the graphene family, 2D metal-organic framework M3 (2,3,6,7,10,11-hexaiminotriphenylene)2 [M3 (HITP)2], 2D transition metal carbides and carbonitrides (MXenes), and the novel 2D material MBenes that are based on boron analogs of MXenes. Our results suggest that these 2D materials can achieve high activity and selectivity in electrochemical reactions under extensive theoretical screening. The family of a single transition metal atom nitrogen co-coordination (MN4)-embedded graphene catalyst is known for its excellent activity, selectivity, and high atomic efficiency in the oxygen reduction reaction (ORR), and systematic theoretical research has proved that ORR works along a complete four-electron transfer pathway in acidic conditions, indicating that direct hydrogenation pathways are preferred over the O2 dissociative mechanism in ORR. Furthermore, 2D metal-organic frameworks M3 (HITP)2 and 2D transition metal carbides (MXenes) have been proven to possess high activity and low overpotentials when used for carbon dioxide electrochemical reduction reactions (CO2 RR). We performed density functional theory (DFT) calculations combined with the theoretical screening method and found that both 2D MOF and MXene materials are promising electrocatalysts for reducing CO2 to produce C1 hydrocarbons. Finally, 2D Metal Boride (MBenes) catalysts have the significant catalytic potential for the electroreduction of CO2 to CH4 ; MBenes are also great prospects for application in efficient electrocatalysts with high activity and high selectivity for the nitrogen reduction reaction (NRR) and nitric oxide reduction (NORR). 2D MBene catalysts have a low limiting potential, and their high selectivity is particularly desirable. Still, challenges surrounding the inadequate understanding of the catalytic mechanism need to be met if these materials are used commercially. To reduce nitric oxide to ammonia by electrochemical conversion as an efficient approach to solving air pollu tion, MBene materials are an attractive electroreduction 5 catalyst with which ammonia can be synthesized from nitric oxide (NO) in a process driven by renewable energy, such as wind and solar power. One promising strategy is the use of the Haber–Bosch process to synthesize ammonia under ambient conditions. Ammonia synthesis depends on the fixation of industrial nitrogen. It is important that the synthesis of chemicals and fertilizers while removing NO to solve air pollution is attractive and challenging in electrocatalysis. Current research generally focuses on these issues separately. However, the direct electrochemical reduction of N2 to NH3 is seldom mentioned. We propose a new electrocatalyst, metal boride (MBene), as a promising candidate catalyst for achieving the direct electroreduction of N2 to NH3. Therefore, our study evaluates a novel 2D material for use as a high-efficiency metal boride (MBene) electrocatalyst that can fix chemical nitrogen and remove NO, purifying exhaust gas. MBenes are also an effective alternative to the Haber–Bosch process currently used to synthesize ammonia

Computational strategies for the accurate thermochemistry and kinetics of gas-phase reactions

This PhD thesis focuses on the theoretical and computational modeling of gas phase chemical reactions, with a particular emphasis on astrophysical and atmospherical ones. The ability to accurately determine the rate coefficients of key elementary reactions is deeply connected to the accurate determination of geometrical parameters, vibrational frequencies and, even more importantly, electronic energies and zeropoint energy corrections of reactants, transition states, intermediates and products involved in the chemical reaction, together with a suitable choice of the statistical approach for the rate computation (i.e. the proper transition state theory model). The main factor limiting the accuracy of this process is the computational time requested to reach meaningful results (i.e. reaching subchemical accuracy below 1 kJ mol−1), which increases dramatically with the the size of the system under investigation. For small-sized systems, several nonempirical procedures have been developed and presented in the literature. However, for larger systems the well-known model chemistries are far from being parameter-free since they include some empirical parameters and employ geometries which are not fully reliable for transition states and noncovalent complexes possibly ruling the entrance channels. Based on these premises, this dissertation has been focused on the development of new “cheap” composite schemes, entirely based on the frozen core coupled cluster ansatz including single, double, and (perturbative) triple excitation calculations in conjunction with a triple-zeta quality basis set, including the contributions due to the extrapolation to the complete basis set limit and core-valence effects using second-order Møller- Plesset perturbation theory. For the first time the “cheap” scheme has been extended to explicitly-correlated methods, which have an improved performance with respect to their conventional counterparts. Benchmarks with different sets of state of the art energy barriers, interaction energies and geometrical parameters spanning a wide range of values show that, in the absence of strong multireference contributions, the proposed models outperforms the most well-known model chemistries, reaching a subchemical accuracy without any empirical parameter and with affordable computer times. Besides the composite schemes development efforts, a robust protocol for disclosing the thermochemistry and kinetics of reactions of atmospheric and astrophysical interest, rooted in the so-called ab initio-transition-state-theory-based master equation approach have been thoroughly investigated and validated