Proteins are dynamic structural entities that are involved in many biophysical processes through molecular interactions with their ligands. Protein-ligand interactions are of fundamental importance for computer-aided drug discovery. Due to the fast development in computer technologies and theoretical methods, computational studies are by now able to provide atomistic-level description of structures, thermodynamic and dynamic properties of protein-ligand systems, and are becoming indispensable in understanding complicated biomolecular systems. In this dissertation, I have applied molecular dynamic (MD) simulations combined with several state of the art free-energy calculation methodologies, to understand structures and binding properties of several protein-ligand systems. The dissertation consists of six chapters. In the first chapter, I present a brief introduction to classical MD simulations, to recently developed methods for binding free energy calculations, and to enhanced sampling of configuration space of biological systems. The basic features, including the Hamiltonian equations, force fields, integrators, thermostats, and barostats, that contribute to a complete MD simulation are described in chapter 2. In chapter 3, two classes of commonly used algorithms for estimating binding free energies are presented. I highlight enhanced sampling approaches in chapter 4, with a special focus on replica exchange MD simulations and metadynamics, as both of them have been utilized in my work presented in the chapter thereafter. In chapter 5, I outlined the work in the 5 papers included in the thesis. In paper I and II, I applied, respectively, the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) and alchemical free energy calculation methods to identify the molecular determinant of the affibody protein ZAb3 bound to an amyloid b peptide, and to investigate the binding profile of the positive allosteric modulator NS-1738 with the α7 acetylcholine-binding protein (α7-AChBP protein); in paper III and VI, unbiased MD simulations were integrated with the well-tempered metadynamics approach, with the aim to reveal the mechanism behind the higher selectivity of an antagonist towards corticotropin-releasing factor receptor-1 (CRF1R) than towards CRF2R, and to understand how the allosteric modulation induced by a sodium ion is propagated to the intracellular side of the d-opioid receptor; in the last paper, I proved the structural heterogeneity of the intrinsically disordered AICD peptide, and then employed the bias-exchange metadynamics and kinetic Monte Carlo techniques to understand the coupled folding and binding of AICD to its receptor Fe65-PTB2. I finally proposed that the interactions between AICD and Fe65-PTB2 take place through an induced-fit mechanism. In chapter 6, I made a short conclusion of the work, with an outlook of computational simulations of biomolecular systems. / <p>QC 20170516</p>

HTML clipboardKinetics on molecular excited states is a challenging subject in the field of theoretical chemistry. This thesis pays attention to theoretical studies on kinetics of photo-induced processes, including photo-chemical reactions, radiative and non-radiative transitions (intersystem crossing and internal conversion) in molecular and bio-related systems. One- or multi- dimensional potential energy surfaces (PESs) not only provide qualitative mechanistic explanation for excited state decay, but also make it possible to perform kinetic simulations. We have constructed several types of PESs by using computational methods of high-accuracy for a variety of systems of interest. In particular, density functional theory (DFT) and couple cluster singles and doubles (CCSD) method are employed to build PESs of the ground and lowest triple states. For medium-sized molecules, the complete active space self-consistent (CASSCF) method is used for constructing the PESs of excited states. Various kinetic theories for the decay processes of excite states are briefly introduced, in particularly adiabatic and nonadiabatic Rice–Ramsperger–Kassel -Marcus (RRKM) approaches for the kinetics of nonradiative decay of excited 2-aminopridine molecule. Special attention has been devoted to Monte Carlo transition state theory which can provide an efficient way to predict the rate of nonradiative transitions of polyatomic molecules on multi-dimensional PESs. Examples of Monte Carlo simulations on the intersystem crossing of isocyanic acid and a model molecule of hexacoordinate heme, as well as internal conversion process for 2-amininopyridine dimer and the adenine-thymine base pair are presented. / QC20100720

Different theoretical approaches have been presented in this thesis to study the Raman scattering effect. The first one is response theory applied up to third order of polarization, where the determination of α, β and γ is used to calculate linear Raman scattering (resonance Raman scattering (RRS) and normal Raman scattering (NRS)), hyper Raman scattering (HRS) and coherent anti-Stokes Raman scattering (CARS), respectively. The response theory refers to adiabatic time-dependent density functional theory in the complex domain with applications on RRS and NRS, and to a recently developed methodology (Thorvaldsen et al. [105, 106]) for the analytic calculation of frequency-dependentpolarizability gradients of arbitrary order, here with applications on CARSand HRS. Various systems have been studied with the response theory, such as explosive substances (DNT, TNT, RDX and H2O2), optical power limiting materials (platinum(II) acetylide molecules), DNA bases (methylguanine-methylcytosine) and other systems (Trans-1,3,5-hexatriene and Pyridine). We have explored the dependency of the calculated spectra on parametrization in terms of exchange-correlation functionals and basis sets, and on geometrica loptimization. The second approach refers to time-dependent wave packet methodology for RRS and its time-independent counterpart in the Kramers-Heisenberg equation for the scattering cross section, which reduces the calculation of the RRS amplitude to computation of matrix elements of transition dipole moments between vibrational wave functions. The time-dependent theory has been used to examine RRS as a dynamical process where particular attention is paid to the notion of fast scattering in which the choice of photon frequency controls the scattering time and the nuclear dynamics. It is shown that a detuning from resonance causes a depletion of the RRS spectrum from overtones and combination bands, a situation which is verified in experimental spectra. The cross section of NRS has been predicted for the studied molecules to be in the order of 10−30 cm2/sr. A further increase in sensitivity with a signal enhancement up to 104 to 105 is predicted for the RRS technique, while CARS conditions imply an overall increase of the intensity by several orders of magnitude over NRS. In contrast to RRS and CARS, the HRS intensity is predicted to be considerably weaker than NRS, by about four orders of magnitude. However, silent modes in NRS can be detected by HRS which in turncan provide essential spectroscopic information and become complementary to NRS scattering. With the above mention methodological development for NRS, RRS, CARS and HRS, we have at our disposal a powerful set of modelling tools for the four different Raman techniques. They have complementary merits and limitations which facilitate the use of these spectroscopes in applications of Raman scattering for practical applications, for instance stand-off detection of foreign substances. / QC 20110112

This thesis focuses on the applications of molecular dynamics simulation techniques in the fields of solution chemistry and atmospheric chemistry. The work behind the thesis takes account of the fast development of computer hardware, which has made computationally intensive simulations become more and more popular in disciplines like pharmacy, biology and materials science. In molecular dynamics simulations using classical force fields, the atoms are represented by mass points with partial charges and the inter-atomic interactions are modeled by approximate potential functions that produce satisfactory results at an economical computational cost. The three-dimensional trajectory of a many-body system is generated by integrating Newton’s equations of motion, and subsequent statistical analysis on the trajectories provides microscopic insight into the physical properties of the system. The applications in this thesis of molecular dynamics simulations in solution chemistry comprise four aspects: the 113Cd nuclear magnetic resonance shielding constant of aqua Cd(II) ions, paramagnetic 19F nuclear magnetic resonance shift in fluorinated cysteine, solvation free energies and structures of metal ions, and protein adsorption onto TiO2. In the studies of nuclear magnetic resonance parameters, the relativistic effect of the 113Cd nucleus and the paramagnetic shift of 19F induced by triplet O2 are well reproduced by a combined molecular dynamics and density functional theory approach. The simulation of the aqua Cd(II) ion is also extended to several other monovalent, divalent and trivalent metal ions, where careful parameterization of the metal ions ensures the reproduction of experimental solvation structures and free energies. Molecular dynamics simulations also provided insight into the mechanism of protein adsorption onto the TiO2 surface by suggesting that the interfacial water molecules play an important role of mediating the adsorption and that the hydroxylated TiO2 surface has a large affinity to the proteins. The applications of molecular dynamics simulations in atmospheric chemistry are mainly focused on two types of organic components in aerosol droplets: humic-like compounds and amino acids. The humic-like substances, including cis-pinonic acid, pinic acid and pinonaldehyde, are surface-active organic compounds that are able to depress the surface tension of water droplets, as revealed by both experimental measurements and theoretical computations. These compounds either concentrate on the droplet surface or aggregate inside the droplet. Their effects on the surface tension can be modeled by the Langmuir-Szyszkowski equation. The amino acids are not strong surfactants and their influence on the surface tension is much smaller. Simulations show that the zwitterionic forms of serine, glycine and alanine have hydrophilic characteristics, while those of valine, methionine and phenylalanine are hydrophobic. The curvature dependence of the surface tension is also analyzed, and a slight improvement in the Köhler equation is obtained by introducing surface tension corrections for droplets containing glycine and serine. Through several examples it is shown that molecular dynamics simulations serve as a promising tool in the study of aqueous systems. Both solute-solvent interactions and interfaces can be treated properly by choosing suitable potential functions and parameters. Specifically, molecular dynamics simulations provide a microscopic picture that evolves with time, making it possible to follow the dynamic processes such as protein adsorption or atmospheric droplet formation. Moreover, molecular dynamics simulations treat a large number of molecules and give a statistical description of the system; therefore it is convenient to compare the simulated results with experimentally measured data. The simulations can provide hints for better design of experiments, while experimental data can be fed into the refinement of the simulation model. As an important complementary to experiments, molecular dynamics simulations will continue to play significant roles in the research fields of physics, chemistry, materials science, biology and medicine. / QC 20110511

his thesis has been devoted to the study of underlying mechanisms for electron transport in molecular electronic devices. Not only has focus been on describing the elastic and inelastic electron transport processes with a Green's function based scattering theory approach, but also on how to construct computational models that are relevant to experimental systems. The thesis is essentially divided into two parts. While the rst part covers basic assumptions and the elastic transport properties, the second part covers the inelastic transport properties and its applications. It is discussed how di erent experimental approaches may give rise to di erent junction widths and thereby di erences in coupling strength between the bridging molecules and the contacts. This di erence in coupling strength is then directly related to the magnitude of the current that passes through the molecule and may thus explain observed di erences between di erent experiments. Another focus is the role of intermolecular interactions on the current-voltage (I-V) characteristics, where water molecules interacting with functional groups in a set of conjugated molecules are considered. This is interesting from several aspects; many experiments are performed under ambient conditions, which means that water molecules will be present and may interfere with the experiment. Another point is that many measurement are done on self-assembled monolayers, which raises the question of how such a measurement relates to that of a single molecule. By looking at the perturbations caused by the water molecules, one may get an understanding of what impact a neighboring molecule may have. The theoretical predictions show that intermolecular e ects may play a crucial role and is related to the functional groups, which has to be taken into consideration when looking at experimental data. In the second part, the inelastic contribution to the total current is shown to be quite small and its real importance lies in probing the device geometry. Several molecules are studied for which experimental data is available for comparison. It is demonstrated that the IETS is very sensitive to the molecular conformation, contact geometry and junction width. It is also found that some of the spectral features that appear in experiment cannot be attributed to the molecular device, but to the background contributions, which shows how theory may be used to complement experiment. This part concludes with a study of the temperature dependence of the inelastic transport. This is very important not only from a theoretical point of view, but also for the experiments since it gives experimentalists a sense of which temperature ranges they can operate for measuring IETS. / QC 20100804. Ändrat titeln från: "Understanding Electron Transport Properties in Molecular Devices" 20100804.

The self-interaction error (SIE) in density functional theory (DFT) appears from the fact that the residual self-interaction in the Coulomb part and that in the exchange part do not cancel each other exactly. This error is responsible for the unphysical orbital energies of DFT and the failure to reproduce the potential energy curves of several physical processes. The present thesis addresses several methods to solve the problem of SIE in DFT. A new algorithm is presented which is based on the Perdew-Zunger (PZ) energy correction and which includes the self-interaction correction (SIC) self-consistently (SC SIC PZ). When applied to the study of hydrogen abstraction reactions, for which conventional DFT can not describe the processes properly, SC PZ SIC DFT produces reasonable potential energy curves along the reaction coordinate and reasonable transition barriers. A semi-empirical SIC method is designed to correct the orbital energies. It is found that a potential coupling term is generally nonzero for all available approximate functionals. This coupling term also contributes to the self-interaction error. In this scheme, the potential coupling term is multiplied by an empirical parameter , introduced to indicate the strength of the potential coupling, and used to correct the PZ SIC DFT. Through a fitting scheme, we find that a unique can be used for C, N, O core orbitals in different molecules. Therefore this method is now used to correct the core orbital energies and relevant properties. This method is both efficient and accurate in predicting core ionization energies. A new approach has been designed to solve the problem of SIE. A functional is constructed based on electron-electron interactions, Coulomb and exchange-correlation parts, which are free of SIE. A post-SCF procedure for this method has been implemented. The orbital energies thus obtained are of higher quality than in conventional DFT. For a molecular system, the orbital energy of the highest occupied molecular orbital (HOMO) is comparable to the experimental first ionization potential energy. / QC 20100915

This thesis presents a theoretical study of the role of nuclear degrees of freedom in the x-ray absorption, x-ray resonant scattering  and some aspects of the interaction of matter with strong laser fields. Most numerical simulations are performed with a time-dependent wave-packet program that have proved its robustness  in previous investigations. The relevant experimental results are also presented for comparison when available. The first problem considered in the thesis is the possibility of obtaining x-ray absorption spectra with resolution beyond the natural lifetime broadening of the core-excited electronic states. It is shown that the method of measuring x-ray absorptionin the resonant scattering mode suggested earlier for that purpose exhibits severe limitations originating from the lifetime vibrational interference between the intermediate core-excited vibrational levels. However, a broad class of molecules is found for which spectra with super-high resolution can indeed be obtained. These molecules have parallel potential energy surfaces of the core-excited and final states for the x-ray scattering process. The interpretations of two interesting cases of x-ray absorption and Auger scattering follow. The first one is related to scattering through a doubly excited Π state in the CO molecule. A Doppler split feature near 299.4 eV and strong scattering anisotropy are  observed. Both features are well explained and reproduced by the theory. Next, theelectron-vibrational fine structure of the <img src="http://www.diva-portal.org/cgi-bin/mimetex.cgi?O1s%5Crightarrow%5Csigma%5E%7B*%7D" /> excitation for O2 is investigated by means of different models. We are able to single out the electronic states and interpotential crossing points responsible for the peculiar absorption profile. Based on these findings we explain and reproduce the x-ray Auger scattering spectra through the same excitation. Here we encounter a rather unusual situation in which the Auger spectra are affected by three types of the interference: Apart from the lifetime vibrational interference, a strong interference between two intermediate electronic states and an interference with the direct-scattering amplitude is also present. The process of intramolecular vibrational redistribution (IVR) is investigated in the context of formation of amplified spontaneous emissions (ASE) inside laser-pumped gain media. IVR raises to a higher energy region the threshold pump intensity after which blue-shifted ASE is observed. Finally, we suggest a new scheme of x-ray pump-probe spectroscopy based on the core-hole hopping in N2 induced by an infrared laser field. We investigate the result from the core-hole hoping on the vibrational structure of the x-ray absorption profile. Furthermore, by populating core-excited states with opposite parities, the laser field opens up symmetry forbidden resonant inelastic scattering channels, which can give new insights about the electronic structure of matter. / QC 20100917

<p>A very important trend for studying biomolecules is computational chemistry. In particular, nowadays it is possible to use theoretical methods to figure out the catalytic mechanism of enzyme reactions. Quantum chemistry has become a powerful tool to achieve a description of biological processes in enzymes active sites and to model reaction mechanisms.</p><p>The present thesis uses Density Functional Theory (DFT) to investigate catalytic mechanism of methyltransferase enzymes. Two enzymes were studied – Glycine N-MethylTransferase (GNMT) and Guanidinoacetate Methyltransferase (GAMT). Different models of the enzyme active sites, consisting of 20 to 100 atoms, are employed. The computed energetics are compared and are used to judge the feasibility of the reaction mechanisms under investigation.</p><p>For the GNMT enzyme, the methyl transfer reaction was found to follow an SN2 reaction mechanism. The calculations demonstrate that the mechanism is thermodynamically reasonable. Based on the calculations it was concluded that hydrogen bonds to the amino group of the glycine substrate lower the reaction barrier, while hydrogen bonds to carboxylate group raise the barrier.</p><p>In the GAMT enzyme the methyl transfer reaction was found to follow a concerted asynchronous mechanism which includes transfer of a methyl group accompanied by a proton transfer taking place simultaneously in the same kinetic step. The calculated barrier agrees well with the experimental rate constant. i</p>

This thesis aims to rationally design nanoparticles and promote their applications in biomedical imaging and photovoltaic cells. Quantum dots (QDs) are promising fluorescent probes for biomedical imaging. We have fabricated two types of MSA capped QDs: CdTe/ZnSe core/shell QDs synthesized via an aqueous method and CdTe QDs via a hydrothermal method. They present high quantum yields (QYs), narrow emission band widths, high photo- and pH-stability, and low cytotoxicity. QD-IgG probes were produced and applied for labeling breast cancer marker HER2 proteins on MCF-7 cells. For the purpose of single molecule tracking using QDs as fluorescent probes, we use small affibodies instead of antibodies to produce QD-affibody probes. Smaller QD-target protein complexes are obtained using a direct immunofluorescence approach. These QD-affibody probes are developed to study the dynamic motion of single HER2 proteins on A431 cell membranes. Fluorescence blinking in single QDs is harmful for dynamic tracking due to information loss. We have experimentally studied the blinking phenomenon and the mechanism behind. We have discovered an emission bunching effect that two nearby QDs tend to emit light synchronously. The long-range Coulomb potential induced by the negative charge on the QD surface is found to be the major cause for the single QD blinking and the emission bunching in QD pairs. We have studied the in vitro cytotoxicity of CdTe QDs to human umbilical vein endothelial cells (HUVECs). The QDs treatment increases the intracellular reactive oxygen species (ROS) level and disrupts the mitochondrial membrane potential. The protein expression levels indicate that the mitochondria apoptosis is the main cause of HUVCEs apoptosis induced by CdTe QDs. Gold nanorods (GNRs) are scattering probes due to their tunable surface plasmon resonance (SPR) enhanced scattering spectrum. In order to control the yield and morphology of GNRs, we have systematically studied the effects of composition and concentration in the growth solution on the quality of the GNRs produced via a seed-mediated method. The aspect ratios of GNRs were found to be linearly depended on the concentration ratio of silver ions and CTAB. The high quality GNRs obtained were adsorbed to COS-7 cell membranes for dark field imaging. We have rationally designed two types of QDs by wave function engineering so as to improve the efficiency of QD-sensitized solar cells. A reversed type-I CdS/CdSe QD confines excitons in the shell region, whereas a type-II ZnSe/CdS QD separates electrons in the shell and holes in the core. Their absorbed photon-to-current efficiencies (APCE) are as high as 40% and 60% respectively. In conclusion, rationally designed nanoparticles are proven a high potential for applications as probes in biomedical labeling, imaging and molecule tracking, and as sensitizers for photovoltaic cells. / QC 20110511

The study of surface adsorption and reaction is not only interesting from a scientific point of view, but also important in many application fields such as energy, environment, catalysis, corrosion, electronic device, and sensor. Theoretical calculations are essential in these studies. In this thesis, first principles studies for the structure and reaction of some important single molecules on the surface are presented. Dehydrogenation of single trans-2-butene molecule on a Pd(110) surface is the first example. The adsorption configurations of both reactant and produce are assigned and the whole dehydrogenation pathway is revealed. Our calculations show that the reactant, i.e. trans-2-butene molecule, undergoes a rotation before dehydrogenation occurs, which is an important detail that cannot be observed directly in scanning tunneling microscopy (STM) experiments. The dissociation and rotation processes of single oxygen molecule on a Pt(111) surface have been a subject of extensive studies in the past. A new intermediate state with a peculiar configuration is identified. The puzzled adsorption site is well explained. The calculated energy barriers agree well with experimental results for both dissociation and rotation processes. Another aspect addressed in this thesis is the mechanism of molecular electronic switches induced by molecular structural changes. By carefully examining the tautomerization process of a naphthalocyanine molecule, an intermediate state is located on the potential surface of the tautomerization. Our calculations indicate that the experimentally observed switching involves four-states, rather than the two-state as proposed by the experimentalists. In a joint experimental and theoretical study the dehydrogenation, tautomerization, and mechanical switching processes of a single melamine molecule on a Cu(100) surface have been comprehensively examined. A new dual-functional molecular device with integrated rectifying and switching functions is made for the first time. In collaborating with another experimental group, we have simulated the switching process of a single 1,1,2,3,4,5-hexaphenylsilole molecule on a Cu(111) surface. The role of the orientation of the molecule is carefully examined and a new switching mechanism is proposed. Switching processes are strongly associated with the inelastic electron tunneling. We have proposed a statistical model that allows explaining the non-integer exponent in the power-law relationship between the switching rate and tunneling current. In this model, the importance of the randomness in inelastic electron excitations and the lifetime of the immediate state are emphasized. It has shown that the inelastic electron tunneling is a collection of various n-electron processes with different statistical weight. / QC 20110524