A5058165123- Advanced Chemical Physics Studies
- Molecular Spectroscopy and Structure
- Spectroscopy and Quantum Chemical Studies
- Protein Structure and Dynamics
- Molecular spectroscopy and chirality
- Algebraic and Geometric Analysis
- Mechanical and Optical Resonators
- Quantum, superfluid, helium dynamics
- Quantum Mechanics and Non-Hermitian Physics
- Enzyme Structure and Function
- Advanced NMR Techniques and Applications
- Geophysics and Sensor Technology
- Mathematics and Applications
- Atmospheric Ozone and Climate
- Geometric and Algebraic Topology
- Astrophysics and Cosmic Phenomena
- Atmospheric aerosols and clouds
- Chemical Reactions and Mechanisms
- Porphyrin and Phthalocyanine Chemistry
- Particle Accelerators and Free-Electron Lasers
- Various Chemistry Research Topics
- Advanced Fiber Laser Technologies
- Amyotrophic Lateral Sclerosis Research
- Advanced Theoretical and Applied Studies in Material Sciences and Geometry
- Quantum and Classical Electrodynamics
University of Helsinki
2002-2025
Ions enhance the formation rate of atmospheric aerosol particles, which play an important role in Earth’s radiative balance. Ion-induced nucleation involves stepwise accretion neutral monomers onto a molecular cluster containing ion, helps to stabilize against evaporation. Although theoretical frameworks exist calculate collision coefficients between molecules and ions, they need be experimentally confirmed, ideally under atmospherically relevant conditions around 1000 ion pairs cm−3. Here,...
Data analysis is a major task for Computational Chemists. The diversity of modeling tools currently available in Chemistry requires the development flexible that can adapt to different systems and output formats. As contribution this need, we report implementation goChem, versatile open-source library multiscale computational chemistry data. library, written Go programming language, allows easy integration levels theory, an easy-to-use API, allowing both one-use complex programs Go. We...
A new inversion coordinate is defined for ammonia as a function of the valence angles. Its square similar to often used totally symmetric bending displacement pyramidal XY3–type molecules. We have this in two-dimensional calculation including stretching and mode. conventional symmetrized internal employed stretch. potential energy surface calculated using ab initio CCSD(T) method together with aug-cc-pVTZ, cc-pVQZ, aug-cc-pVQZ basis sets. The corresponding eigenvalues are variationally Morse...
Eckart frame is a unique embedding in the theory of molecular vibrations and rotations. It defined by condition that Coriolis coupling reference structure molecule zero for every choice shape coordinates. far from trivial to set up kinetic energy operators (KEOs), when described curvilinear In order obtain KEO, one needs corresponding contravariant metric tensor. Here, I derive explicitly rotational measuring vectors. Their inner products with themselves give elements, their vibrational...
The gradients of vibrational coordinates are needed in order to form the exact kinetic energy operator a polyatomic molecule. conventional methods used obtain these often quite laborious. However, by geometric algebra, for any coordinate can be easily calculated. Examples given, and special attention is directed ring coordinates.
The elements of the reciprocal metric tensor g(qiqj), which appear in exact internal kinetic energy operators polyatomic molecules can, principle, be written as mass-weighted sum inner products measuring vectors associated to nuclei molecule. In case vibrational degrees freedom, are simply gradients coordinates. It is more difficult find these for rotational because components total angular momentum operator not conjugated any However, by methods geometric algebra, easily calculated...
It is a common approach in quantum chemical calculations for polyatomic molecules to rigidly constrain some of the degrees freedom order make computationally feasible. However, presence rigid constraints also affects kinetic energy operator resulting frozen mode correction, originally derived by Pesonen [J. Chem. Phys. 139, 144310 (2013)]. In this study, we compare effects correction several different approximations used literature, specific case rotamer levels sulfuric acid. The two stable...
Abstract The small‐amplitude conformational changes in macromolecules can be described by the bond lengths and angles. descriptors of large scale are torsions. We present a recursive algorithm, which vector is explicitly written terms these internal, or polyspherical coordinates, local frame defined two other vectors their cross product. Conformations linear branched molecules, as well molecules containing rings this way. orientation molecule body frame. It parametrized instantaneous...
In this work, geometric algebra is applied to obtain the volume-element of integration for 3 Cartesian coordinates center-of-mass, Euler angles, and 3N−6 shape needed describe position, orientation, an N-atomic molecule. The obtained as a product N volume-elements, each associated with set three coordinates. method presented has several advantages. For example, one does not need expand any determinants, all calculations are performed in three-dimensional physical space (not some...
It is customary to describe molecular vibrations using as exact kinetic energy operators and accurate potentials possible. has become a standard approach express Hamiltonians in curvilinear internal displacement coordinates, because they offer simple physical picture of vibrational motions, including large amplitude changes the shape. In older normal mode model vibrations, nuclei are thought vibrate infinitesimally about reference configuration, shape molecule described linearized...
Here, I present a practical recipe for obtaining contravariant vibration-rotation metric tensors, and thus the kinetic energy operators, when some degrees of freedom are constrained rigidly. An element tensor is obtained as sum dot products measuring vectors, which from their unconstrained counterparts by adding frozen mode correction. The method applies in principle any choice shape coordinates body-frame vectors can be evaluated. In contrast to existing methods, does not involve evaluation...
The gradients of vibrational coordinates are needed in order to form the exact kinetic energy operator a polyatomic molecule. In my previous work [J. Chem. Phys. 112, 3121 (2000)], it was demonstrated that they can be easily obtained for any geometrically defined shape by direct vectorial differentiation. However, there is some cases more practical way obtain these from variation along path particle. This approach used effectively find coordinates, which given as implicit functions nuclear...
Abstract The large scale motion of proteins, or covalently bonded polymers in general, is governed by the dynamics torsion angles, with bond lengths and angles kept approximately constant. In present work, Lagrangian equations are derived for a general macromolecule. implemented numerically test protein, using velocity Verlet method as integrator. results indicate time steps up to about 30 fs can be used short (up at least 20 ps) simulations, before energy start differ significantly from...
The suitability of a recently developed extension to the polyspherical parametrization protein complexes has been investigated by molecular dynamic simulations. makes it possible study motion proteins consisting several chains, which are internally covalently bonded. Tests indicate that time steps up at least 10 fs for simulations lasting 100 ps possible, small proteins.
In this work, I present a practical way to obtain the vibration-rotation kinetic energy operator for an N-atomic molecule in arbitrary body-frame [Formula: see text]. The need not be orthogonal or rigid. practice, derive explicit form of measuring vectors associated with components internal angular momentum. Their inner products vector derivatives shape coordinates give "Coriolis" part metric tensor appearing Hamiltonian, and their among themselves "rotational" part. As simple example, are...
Abstract Two-centre integrals involving displaced and distorted (or squeezed) simple harmonic oscillator number states, the DSN are often encountered in molecular spectroscopy quantum theory of wave packets light. For example, Franck–Condon factors overlap states. In this work, finite, closed algebraic formulas derived for overlap, exponential, trigonometric polynomial integrals. Acknowledgements Andrea Beddoni acknowledges support EU under RTN program 5 (contract No. HPRN-CT-1999-00005)....