Role of quantum chemical calculations in molecular biophysics with a historical perspective

We discuss how the basic principles of quantum chemistry and quantum mechanics can be and have been applied to a variety of problems in molecular biophysics. First, the historical development of quantum concepts in biophysics is discussed. Next, we describe a series of interesting applications of quantum chemical methods for studying biologically active molecules, molecular structures, and some of the important processes which play a role in living organisms. We discuss the application of quantum chemistry to such processes as energy storage and transformation, and the transmission of genetic information. Quantum chemical approaches are essential to comprehend and understand the molecular nature of these processes. To conclude our work, we present a short discussion of the perspectives of quantum chemical methods in modern biophysics, the field of experimental and theoretical chiral vibrational and electronic spectroscopy

Effects of mannose, fructose, and fucose on the structure, stability, and hydration of lysozyme in aqueous solution

The bio-protective properties of monosaccharaides, namely mannose, fructose and fucose, on the stability and dynamical properties of the NMR determined hen egg-white lysozyme structure have been investigated by means of molecular dynamics simulations at room temperature in aqueous solution and in 7 and 13 wt % concentrations of the three sugars. Results are discussed in the framework of the bio-protective phenomena. The three sugars show similar bio-protective behaviours at room temperature (300 K) in the concentration range studied as shown by the small RMSDs of the resulting MD structures from that of starting NMR structure. The effects of sugars on protein conformation are found to be relatively strong in that the conformation of lysozyme is stable after an initial 9 ns equilibration for fucose and mannose and 12 ns equilibration for fructose, respectively, at high concentrations. For mannose the final RMSD is significantly smaller than that of fucose and fructose at the higher concentration, while at the lower concentration the RMSD are essentially the same. The radial distribution function of the water and sugars around lysozyme was used to monito

First principles structures and circular dichroism spectra for the close-packed and the 7/2 motif of collagen

The recently proposed close-packed motif for collagen is investigated using first principles semi-empirical wave function theory and Kohn-Sham density functional theory. Under these refinements the close-packed motif is shown to be stable. For the case of the 7/2 motif a similar stability exists. The electronic circular dichroism of the close-packed model has a significant negative bias and a large signal. An interesting feature of the close-packed structure is the existence of a central channel. Simulations show that, if hydrogen atoms are placed in the cavity, a chain of molecular hydrogens is formed suggesting a possible biological function for molecular hydrogen.Comment: 12 pages, 3 figures; 3(PPG)_6 xyz file attached; v2: minor modification

Modeling of the Concentrations of Ultrafine Particles in the Plumes of Ships in the Vicinity of Major Harbors

Marine traffic in harbors can be responsible for significant atmospheric concentrations of ultrafine particles (UFPs), which have widely recognized negative effects on human health. It is therefore essential to model and measure the time evolution of the number size distributions and chemical composition of UFPs in ship exhaust to assess the resulting exposure in the vicinity of shipping routes. In this study, a sequential modelling chain was developed and applied, in combination with the data measured and collected in major harbor areas in the cities of Helsinki and Turku in Finland, during winter and summer in 2010-2011. The models described ship emissions, atmospheric dispersion, and aerosol dynamics, complemented with a time-microenvironment-activity model to estimate the short-term UFP exposure. We estimated the dilution ratio during the initial fast expansion of the exhaust plume to be approximately equal to eight. This dispersion regime resulted in a fully formed nucleation mode (denoted as Nuc(2)). Different selected modelling assumptions about the chemical composition of Nuc(2) did not have an effect on the formation of nucleation mode particles. Aerosol model simulations of the dispersing ship plume also revealed a partially formed nucleation mode (Nuc(1); peaking at 1.5 nm), consisting of freshly nucleated sulfate particles and condensed organics that were produced within the first few seconds. However, subsequent growth of the new particles was limited, due to efficient scavenging by the larger particles originating from the ship exhaust. The transport of UFPs downwind of the ship track increased the hourly mean UFP concentrations in the neighboring residential areas by a factor of two or more up to a distance of 3600 m, compared with the corresponding UFP concentrations in the urban background. The substantially increased UFP concentrations due to ship traffic significantly affected the daily mean exposures in residential areas located in the vicinity of the harbors.Peer reviewe

Kolsänkan av levande biomassa i fjällnära skog

The study focuses on facts about the role of the forests, near the mountains in the northwestern part of Sweden, from a climate perspective. This refers to the net removal in living tree biomass while the substitution effect is omitted. The area-based (design based) estimates are based on data from the Swedish National Forest Inventories permanent sample plots in two areas close to the mountains. The first area refers to the above limit for forests close to the mountains (above GFS) according to the Swedish Forest Agency and the second according to a map layer that is considered important of protection for biodiversity reasons according to the Swedish Environmental Protection Agency (SEPA). Of the 8.1 Mha of land above the limit for forests close to mountains, 3.1 Mha is forest land, of which 1.7 Mha is formally protected forest land. Productive forest land used for timber production amounts to less than 0.5 Mha. For both formally protected forest land and non-formally protected forest land, living biomass constitutes a net uptake of -1 Mton CO2 / year during the period 1990-2016 on a reasonably similar area. If all forest land above GFS is excluded from timber production, the short-term increase in net removal in the forest will be approximately -0.4 Mton CO2 / year, which corresponds to harvest. Then we do not expect any substitution effect and believe that other carbon pools (dead wood, soil, litter and the carbon pool harvested wood products) in the short term are not affected by the stopping of felling. The Swedish Environmental Protection Agency has selected an area close to the mountains where two thirds comprise forest land. No land is formally protected. Of approximately 1.0 Mha of forest land, 0.39 Mha was assessed as forest land for timber production. The net uptake in living biomass of forest land amounted to approximately -1 Mton CO2 / year during the period. On productive forest land for timber production, the net uptake was approximately -0.6 Mton CO2 / year during the period. If all forest land according to the map layer is excluded from timber production, the short-term increase in net removal in the forest will be approximately -0.1 Mton CO2 / year, which corresponds to harvest. Then we do not expect any substitution effect and believe that other carbon pools in the short term are not affected by the stopping of felling.The study focuses on facts about the role of the forests, near the mountains in the northwestern part of Sweden, from a climate perspective. This refers to the net removal in living tree biomass while the substitution effect is omitted. The area-based (design based) estimates are based on data from the Swedish National Forest Inventories permanent sample plots in two areas close to the mountains. The first area refers to the above limit for forests close to the mountains (above GFS) according to the Swedish Forest Agency and the second according to a map layer that is considered important of protection for biodiversity reasons according to the Swedish Environmental Protection Agency (SEPA). Of the 8.1 Mha of land above the limit for forests close to mountains, 3.1 Mha is forest land, of which 1.7 Mha is formally protected forest land. Productive forest land used for timber production amounts to less than 0.5 Mha. For both formally protected forest land and non-formally protected forest land, living biomass constitutes a net uptake of -1 Mton CO2 / year during the period 1990-2016 on a reasonably similar area. If all forest land above GFS is excluded from timber production, the short-term increase in net removal in the forest will be approximately -0.4 Mton CO2 / year, which corresponds to harvest. Then we do not expect any substitution effect and believe that other carbon pools (dead wood, soil, litter and the carbon pool harvested wood products) in the short term are not affected by the stopping of felling. The Swedish Environmental Protection Agency has selected an area close to the mountains where two thirds comprise forest land. No land is formally protected. Of approximately 1.0 Mha of forest land, 0.39 Mha was assessed as forest land for timber production. The net uptake in living biomass of forest land amounted to approximately -1 Mton CO2 / year during the period. On productive forest land for timber production, the net uptake was approximately -0.6 Mton CO2 / year during the period. If all forest land according to the map layer is excluded from timber production, the short-term increase in net removal in the forest will be approximately -0.1 Mton CO2 / year, which corresponds to harvest. Then we do not expect any substitution effect and believe that other carbon pools in the short term are not affected by the stopping of felling

Impact of a nitrogen emission control area (NECA) on the future air quality and nitrogen deposition to seawater in the Baltic Sea region

Air pollution due to shipping is a serious concern for coastal regions in Europe. Shipping emissions of nitrogen oxides (NOx) in air over the Baltic Sea are of similar magnitude (330&thinsp;kt yr−1) as the combined land-based NOx emissions from Finland and Sweden in all emission sectors. Deposition of nitrogen compounds originating from shipping activities contribute to eutrophication of the Baltic Sea and coastal areas in the Baltic Sea region. For the North Sea and the Baltic Sea a nitrogen emission control area (NECA) will become effective in 2021; in accordance with the International Maritime Organization (IMO) target of reducing NOx emissions from ships. Future scenarios for 2040 were designed to study the effect of enforced and planned regulation of ship emissions and the fuel efficiency development on air quality and nitrogen deposition. The Community Multiscale Air Quality (CMAQ) model was used to simulate the current and future air quality situation. The meteorological fields, the emissions from ship traffic and the emissions from land-based sources were considered at a grid resolution of 4×4&thinsp;km2 for the Baltic Sea region in nested CMAQ simulations. Model simulations for the present-day (2012) air quality show that shipping emissions are the major contributor to atmospheric nitrogen dioxide (NO2) concentrations over the Baltic Sea. In the business-as-usual (BAU) scenario, with the introduction of the NECA, NOx emissions from ship traffic in the Baltic Sea are reduced by about 80&thinsp;% in 2040. An approximate linear relationship was found between ship emissions of NOx and the simulated levels of annual average NO2 over the Baltic Sea in the year 2040, when following different future shipping scenarios. The burden of fine particulate matter (PM2.5) over the Baltic Sea region is predicted to decrease by 35&thinsp;%–37&thinsp;% between 2012 and 2040. The reduction in PM2.5 is larger over sea, where it drops by 50&thinsp;%–60&thinsp;% along the main shipping routes, and is smaller over the coastal areas. The introduction of NECA is critical for reducing ship emissions of NOx to levels that are low enough to sustainably dampen ozone (O3) production in the Baltic Sea region. A second important effect of the NECA over the Baltic Sea region is the reduction in secondary formation of particulate nitrate. This lowers the ship-related PM2.5 by 72&thinsp;% in 2040 compared to the present day, while it is reduced by only 48&thinsp;% without implementation of the NECA. The effect of a lower fuel efficiency development on the absolute ship contribution of air pollutants is limited. Still, the annual mean ship contributions in 2040 to NO2, sulfur dioxide and PM2.5 and daily maximum O3 are significantly higher if a slower fuel efficiency development is assumed. Nitrogen deposition to the seawater of the Baltic Sea decreases on average by 40&thinsp;%–44&thinsp;% between 2012 and 2040 in the simulations. The effect of the NECA on nitrogen deposition is most significant in the western part of the Baltic Sea. It will be important to closely monitor compliance of individual ships with the enforced and planned emission regulations.</p