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13
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5answers
3k views

Does there exist a free good molecule / atom simulation software?

I'm looking for a software or software package (for example C/C++) that can simulate a lot (say thousands at least) of molecules in action (ie. in movement or attached to say static walls). I have ...
13
votes
3answers
389 views

Chemical reaction as state transition?

When considering diffusion of chemicals, the reaction part is business of chemical kinetics, where the relevant characteristics of different substances come from collision theory together with some ...
11
votes
2answers
846 views

Is there experimental verification of the s, p, d, f orbital shapes?

Have there been any experiments performed (or proposed) to prove that the shapes of the s,p,d,f orbitals correspond to our spatial reality as opposed to just being a figment of the mathematics that ...
9
votes
4answers
6k views

Why do covalent bonds form?

why in a covalent bond are "the bonded electrons are in a lower energy state than if the individual atoms held them at the same proximity"? Also is it correct that " I think when you start pushing ...
9
votes
3answers
2k views

What is the quantum mechanical explanation of the octet rule?

What is the quantum mechanical explanation of the octet rule? In other words, what makes the octet rule be true from a quantum mechanical view? How we explain what makes some atoms don't follow the ...
9
votes
2answers
987 views

Why does iteratively solving the Hartree-Fock equations result in convergence?

[ Cross-posted to the Computational Science Stack Exchange: http://scicomp.stackexchange.com/questions/1297/why-does-iteratively-solving-the-hartree-fock-equations-result-in-convergence ] In the ...
6
votes
1answer
246 views

The Born-Oppenheimer approximation and muonic molecules

Does the Born-Oppenheimer approximation fail for muonic molecules (i.e. molecules where one or more electrons are replaced with muons)?
6
votes
2answers
1k views

Is Palladium an exception?

I have been taught in school that atoms cannot have more than 8 electrons in the outer shell. Palladium atom's electron configuration is 2,8,18,18. Why isn't it 2,8,18,17,1 like the case of Platinum ...
5
votes
4answers
670 views

Why is quantum physics needed to explain photosynthesis?

Why is quantum physics needed to explain photosynthesis? In what aspect does the corresponding classical theories for photosynthesis fail?
4
votes
2answers
2k views

Software to simulate and visualize atoms?

Not sure if this is a physics or chemistry question. But if the motion of atoms and it's particles can be described by quantum mechanics, then is there a software that simulate full atoms and it's ...
4
votes
1answer
545 views

Number of unique 2-electron integrals

Consider 2-electron integrals over real basis functions of the form $$(\mu\nu|\lambda\sigma) = \int d\vec{r}_{1}d\vec{r}_{2} \phi_{\mu}(\vec{r}_{1}) \phi_{\nu}(\vec{r}_{1}) r_{12}^{-1} ...
4
votes
1answer
677 views

Can we model Chemical Reactions using Quantum Mechanics? If so, what is the most complex reaction we can model?

Not a physicist or Chemist, just interested in QM and it's applications. I've been reading lately about Quantum Chemistry and it occurred to me that since we can model electron orbitals in QM and ...
4
votes
1answer
255 views

Physical Chemistry: What's the relationship between orbital overlap and barrier shape?

This is a question for the physical chemists out there. For a given chemical reaction there is a barrier to traverse in order to proceed from reactants to products. Reactants e.g. an organic base ...
3
votes
3answers
2k views

1D Infinite Square Well: Box Suddenly Increases in Size. How treat this?

I am currently working my way through John S. Townsend book "A Fundamental Approach to Modern Physics" (ISBN: 978-1-891389-62-7). Exercise 3.12 (p.111) is about the 1D infinite square well. The box ...
3
votes
1answer
198 views

What determines the form of the intensity curves in Laser-Induced Fluorescence (LIF) measurements?

What determines the form of the intensity spectra of different particle species in Laser-Induced Fluorescence (LIF) measurements? See e.g. I figure that bigger particles have more ways to get ...
3
votes
1answer
7k views

Why is oxygen in a triplet state and what are the consequences?

From Wikipedia here and here: ''Almost all molecules encountered in daily life exist in a singlet state, but molecular oxygen is an exception.'' ''The unusual electron configuration prevents ...
3
votes
1answer
140 views

Experiment to find structure of water

Who first determined the structure of water (two hydrogen atoms stuck to an oxygen atom at approx 105 degrees), and, more importantly, how was this done?
3
votes
1answer
184 views

The Physics Behind Chemical Bonding

Ok so here's the problem: say I'm a sodium atom. It is 'charged' at +1e. A partner Chlorine atom is flying about, also 'charged' at -1e. According to chemistry (or rather the measurement of the ...
3
votes
1answer
146 views

Proving that the electronic Schrödinger equation has no closed analytic solutions for >1 electron

It is stated in many books that analytic closed solutions to the time-independent electronic Schrödinger equation, $$\hat{H}\Psi = E\Psi, $$ exist for the one-electron problem (e.g. hydrogen atom, ...
3
votes
1answer
350 views

Why do hydrogen atoms attract?

That is, why is the potential energy with the orbitals overlapping less than with the Hydrogen atoms 'independent'. Similarly, why is a noble gas configuration stabler than if an electron were to be ...
3
votes
0answers
93 views

Quantum Mechanical Thinking

I've just been wondering about how atoms and molecules can be quantum mechanically thought about, and I have a question. It is often said that intermolecular bonding is purely "electrostatic". I hope ...
2
votes
4answers
405 views

Two soft questions about spin and the particle nature of electrons

How can we define spin as the spin of an electron around it's own axis if an electron is described by a probability cloud of finding an electron in a point in space? How does that probability cloud ...
2
votes
2answers
1k views

Changes in Water Bonding Angle

I heard something recently in a casual discussion, but have yet to be able to confirm it: is there any evidence that the bonding angle for a water molecule, currently defined as 104.5, has been either ...
2
votes
6answers
377 views

Rutherford's gold foil experiment: can alphas be deflected by electrons vs. nucleus?

In this experiment, is it possible that some of the alpha particles are deflected by the electrons? Gold, after all, usually also has ~79 of them in each atom. Since the alpha particles want ...
2
votes
1answer
377 views

Why are do neutral atoms shrink as their valence shells approach 8 electrons?

Why do neutral, unbonded atoms shrink in size as they approach having 8 electrons in their valence shells? A good example is elements 3 through 10 in this table, that is, lithium (1 valence electron) ...
2
votes
1answer
208 views

THT (Tetrahydrothiophene) absorption spectrum

I am looking for the absorption spectrum of THT. What is the best way to find these types of exotic material's spectral characteristics?
2
votes
1answer
105 views

What is the difference between real orbital & complex orbital?

While reading Atomic orbitals, I came before these two terms. The 'real orbital' is given here: Real orbitals An atom that is embedded in a crystalline solid feels multiple preferred axes, ...
2
votes
1answer
334 views

Ground state energy of hydrogen molecule ion

In this paper, it is mentioned: Furthermore, since the energy of $H_2^+$in the ground state must be lower than that of an H atom in the ground state,the negative (attractive) forces in the ...
2
votes
1answer
419 views

Minimizing the energy of a Slater determinant: why are the Lagrange multiplier elements of a Hermitian matrix?

If I want to minimize the energy of a Slater determinant subject to the constraint that the spin orbitals are orthonormal (as in the Hartree-Fock approximation), I can use Lagrange's method of ...
2
votes
1answer
209 views

Is it possible to mechanically isomerize an sp3 hybridized carbon center?

Imagine I have an sp3 hybridized carbon attached to four separate polyethylene chains. By pulling on the polyethylene chains in some manner, is it possible for me to mechanically isomerize the chiral ...
2
votes
2answers
101 views

Wavefunction of isomers

In quantum chemistry, the wavefunction for a molecule can be viewed as the output of a function $\xi(m, n_1,..., n_k)$ with $m, n_i \in \mathbb{Z}^+$ that returns a $|\psi\rangle$ that satisfies a ...
2
votes
1answer
88 views

Why does bringing N 1-orbital atoms together yield N levels?

A common example of this is that when bringing N hydrogen atoms together into a ring. Far apart, assume each electron exists in the 1s state. As we bring them together, instead of each electron ...
2
votes
1answer
688 views

Theoretical treatment of Hydrogen bond?

I would like to understand how the Hydrogen bond can be described through the Schroedinger equation. I don't need numerical methods that one uses them to simulate it, rather I need its treatment from ...
2
votes
2answers
131 views

Driving a solution of optical isomer molecules with the resonant frequency

What happens when we drive a solution of optical isomer molecules (enantiomers) with a microwave radiation in resonance with the tunneling frequency of the molecules (the frequency of the transition ...
2
votes
0answers
36 views

Why is the activation energy of combustion so large compared with regular bonding?

I wanted to know why combustion requires an activation energy and I found this article (see this too). It says that molecular oxygen ground state is a triplet state (according to Hund's rules), and ...
2
votes
0answers
9 views

What would be the Slater's determinant of an excited state? [duplicate]

Setup Introducing this spinorbital notation: \begin{align} \Psi_1=\chi_{(r1)}\alpha_{(\omega1)} &= 1 \\ \Psi_1=\chi_{(r1)}\beta_{(\omega1)} &= \bar{1} \end{align} and the Slater's ...
2
votes
0answers
50 views

Geometric measure of entanglement for fermions or bosons?

For a system consisting of multiple components, say, a spin chain consisting of $N\geq 3 $ spins, people sometimes use the so-called geometric measure of entanglement. It is related to the inner ...
2
votes
0answers
34 views

Coefficients and Parameters for contracted Gaussian basis sets

This is a repost from Chemistry.stackexchange in the hopes that someone here will be able to help me. Any help at all would be greatly appreciated. As far as I understand, an STO-NG contracted ...
2
votes
1answer
326 views

Why do electrons couple in atoms?

In describing electron states in hydrogen, we have a very "simple" picture, at least in intro-quantum. But this only has one electron! As we permit more electrons, we also have things like the ...
1
vote
5answers
451 views

What laws (formulas) govern forces between atoms?

What laws (formulas) govern the fundamental forces of nature? For example, gravity is governed by the inverse-square law. I am thinking about how particles attract each other, but also repel. All ...
1
vote
1answer
136 views

How many wavefunctions are in a minimal basis set for benzene?

I am reading Modern Quantum Chemistry by Szabo and Ostlund and on page 62 he says "A minimal basis set for benzene consists of 72 spin orbitals." I tried to understand this number but failed. ...
1
vote
1answer
159 views

Meaning of $C$ in wavefunction equation ($\Psi_{MO} = C_1\phi_A(1s) + C_2\phi_B(1s)$, where $C_1=\pm C_2$)

I've just cracked open a biophysics textbook and it's all fine up until the introduction of the letter C in a wavefunction equation, and declaring C1= ±C2 I've had lectures on eigenfunctions etc. ...
1
vote
1answer
188 views

Coulomb interaction and conservation laws

In many-body solid-state physics, the Coulomb interaction term in the Hamiltonian usually implies the momentum conservation law in indicies: $$H_c=\frac{1}{2} \sum_{\mathbf{k},\mathbf{k}',\mathbf{q} ...
1
vote
2answers
87 views

Atomic orbitals

I just studied atomic orbitals in a theoretical QM class, and I'm left with several questions, that are probably more questions in quantum chemistry: Many orbitals seem to have a preferred axis - ...
1
vote
1answer
96 views

Does O$^{2-}$ really exist?

In chemistry it is common sense that we have O$^{2-}$. But from a physical point of view, does O$^{2-}$ really exist as a negative ion? I mean, as an isolated ion. It is not apparent that a neutral ...
1
vote
1answer
168 views

Chemistry from a physical perspective [duplicate]

I'm currently learning chemistry for the first time, and loving it. I have a reasonably good physics and maths background and it's great to see things like spherical harmonics in quantum mechanics ...
1
vote
1answer
74 views

The Molecular Hamiltonian and the avoidance of Overcounting

Whenever I see the total non-relativistic molecular Hamiltonian, $\hat{H}_{molecular} = \hat{T}_{e} + \hat{T}_{n} + \hat{V}_{ee} + \hat{V}_{nn} + \hat{V}_{en}$ I always notice that the sums ...
1
vote
2answers
93 views

How to use Hartree-Fock for helium?

I am thinking of using Hartree-Fock approximation to calculate the ground state energy of helium. The ground state wave function must have a symmetric orbital wave function. But in HF we need a Slater ...
1
vote
3answers
259 views

Electron in a covalent bond: what happens when it moves out?

Let's look at a covalent bond in, say, a water molecule: H : O : H H is bonded to O by a pair of electrons. But electrons are in constant motion. What happens when the electron leaves? Why does ...
1
vote
1answer
141 views

Does spin alone have any effect on the physical interactions of particles?

In Hartree-Fock theory the time-independent electronic energy of a single (restricted) determinant electronic wavefunction consists of one electron terms, $h_{ii}$, Coulomb interaction energies, ...